brianpardy's vcf_data data (filename: "hu9B93D0.vcf.gz")

Variant

Allele Freq

Info

chr22:g.24109722G>A

ClinVar: NM_001301339.1(CHCHD10): c.100C>T (p.Pro34Ser)

Heterozygous

0.001750

Disease:	Frontotemporal dementia and/or amyotrophic lateral sclerosis
Inheritance:	dominant
Significance:	causal
Evidence:	reported
Clinvar records:	Likely benign: not specified Pathogenic: Frontotemporal dementia and/or amyotrophic lateral sclerosis 2 (FTDALS2)
Notes:	Found in 2 unrelated patients of a screen of 94, and the authors (https://www.ncbi.nlm.nih.gov/pubmed/25155093) seem to propose a dominant effect. But according to other databases this variant is relatively common (1 in 450 are carriers); this frequency in the general population is not mentioned by the study. This may be a contradiction of the reported effect: a disease-causing mutation carried by 1 in 450 individuals would typically be a phenomenon well-characterized by various studies.

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Clinvar entries without associated notes:

Likely benign:

chr3:g.49209095C>T

ClinVar: NM_173546.2(KLHDC8B): c.-158C>T

Heterozygous

0.005235

Disease:	Hodgkin lymphoma
Inheritance:	other/unknown
Significance:	risk factor
Evidence:	contradicted
Clinvar records:	Pathogenic: Hodgkin lymphoma (CHL)
Notes:	OMIM records this as a high penetrance variant, but this is based on a single 2009 paper (https://www.ncbi.nlm.nih.gov/pubmed/19706467) which reported it as a potential risk factor. It was found it carried by 3 of 52 patients, compared with 4 of 307 controls. The authors imply a significant enrichment, but a two-tailed Fisher's Exact test yields p = 0.0657. No follow-up studies that confirm this speculation nor any other involvement of this gene with the disease. This speculated effect should probably be considered contradicted or unsupported.

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chr21:g.35821680C>T

ClinVar: NM_000219.5(KCNE1): c.253G>A (p.Asp85Asn)

Heterozygous

0.008109

Disease:	Long QT syndrome
Inheritance:	dominant
Significance:	causal
Evidence:	contradicted
Clinvar records:	risk factor: Long QT syndrome 5, acquired, susceptibility to Pathogenic: Long QT syndrome 2/5 (LQT2/5, DIGENIC) Benign/Likely benign: not specified Likely benign: Cardiovascular phenotype Likely benign: Romano-Ward syndrome (RWS) Likely benign: Jervell and Lange-Nielsen syndrome (JLNS) Conflicting interpretations of pathogenicity, risk factor: Long QT syndrome (LQTS) Uncertain significance, other: not provided
Notes:	Roughly 1 in 55 individuals carry this variant. OMIM describes one paper claiming this is causal for long QT syndrome, seen twice in a screen of 32 patients (https://www.ncbi.nlm.nih.gov/pubmed/14760488). However this frequency is very similar to the frequency in the general population, and much higher than the rarity of this condition. And almost all labs that have reviewed this variant in ClinVar have classified it as "benign".

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chr1:g.159175494C>T

ClinVar: NM_002036.3(ACKR1): c.265C>T (p.Arg89Cys)

Heterozygous

0.010695

Clinvar entries without associated notes:

Pathogenic: DUFFY BLOOD GROUP SYSTEM, FY(bwk) PHENOTYPE

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chr5:g.142780339C>T

ClinVar: NM_001018077.1(NR3C1): c.66G>A (p.Glu22=)

Heterozygous

0.017758

Clinvar entries without associated notes:

Pathogenic: Glucocorticoid resistance, relative
Likely benign: Glucocorticoid resistance, generalized (GCCR)

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chr11:g.18303533G>A

ClinVar: NM_181507.1(HPS5): c.3293C>T (p.Thr1098Ile)

Heterozygous

0.023903

Clinvar entries without associated notes:

Likely benign: Hermansky-Pudlak syndrome (HPS1)
Pathogenic: Hermansky-Pudlak syndrome 5 (HPS5)
Benign: not specified

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chr6:g.18139228C>T

ClinVar: NM_000367.4(TPMT): c.460G>A (p.Ala154Thr)

Heterozygous

0.024611

Clinvar entries without associated notes:

drug response: Thiopurine methyltransferase deficiency (THPM1)
drug response: Thiopurine methyltransferase deficiency (THPM1)
other: not provided

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chr1:g.156848918C>T

ClinVar: NM_002529.3(NTRK1): c.1810C>T (p.His604Tyr)

Heterozygous

0.036946

Clinvar entries without associated notes:

Pathogenic: Familial medullary thyroid carcinoma (MTC)
Pathogenic: Hereditary insensitivity to pain with anhidrosis (CIPA)
Benign: not specified
Benign/Likely benign: Hereditary insensitivity to pain with anhidrosis (CIPA)

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chr1:g.156848946G>T

ClinVar: NM_001007792.1(NTRK1): c.1730G>T (p.Gly577Val)

Heterozygous

0.037055

Clinvar entries without associated notes:

Pathogenic: Familial medullary thyroid carcinoma (MTC)
Pathogenic: Hereditary insensitivity to pain with anhidrosis (CIPA)
Benign: not specified
Benign/Likely benign: Hereditary insensitivity to pain with anhidrosis (CIPA)

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chr6:g.18130918T>C

ClinVar: NM_000367.4(TPMT): c.719A>G (p.Tyr240Cys)

Heterozygous

0.040801

Clinvar entries without associated notes:

drug response: Thiopurine methyltransferase deficiency (THPM1)
drug response: Thiopurine methyltransferase deficiency (THPM1)
other: not provided

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chr1:g.161518333A>T

ClinVar: NM_001127593.1(FCGR3A): c.197T>A (p.Leu66His)

Heterozygous

0.047996

Clinvar entries without associated notes:

Pathogenic: Immunodeficiency 20 (IMD20)
Uncertain significance: not specified

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chr10:g.54531242G>A

ClinVar: NM_000242.2(MBL2): c.154C>T (p.Arg52Cys)

Heterozygous

0.048656

Clinvar entries without associated notes:

Pathogenic: Mannose-binding protein deficiency (MBLD)

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chr9:g.116153891C>G

ClinVar: NM_000031.5(ALAD): c.177G>C (p.Lys59Asn)

Heterozygous

0.055710

Clinvar entries without associated notes:

Pathogenic: AMINOLEVULINATE DEHYDRATASE, ALAD*1/ALAD*2 POLYMORPHISM
Likely benign: Porphobilinogen synthase deficiency

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chr21:g.46931109G>A

ClinVar: NM_030582.3(COL18A1): c.4309G>A (p.Asp1437Asn)

Heterozygous

0.065757

Disease:	Knobloch syndrome
Inheritance:	recessive
Significance:	causal
Evidence:	contradicted
Clinvar records:	Pathogenic: Knobloch syndrome 1 (KNO1)
Notes:	Very common variant (1 in 90 Europeans is homozygous), contradicting the reported effect.

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Clinvar entries without associated notes:

Benign: not specified

chr11:g.68562328C>T

ClinVar: NM_001876.3(CPT1A): c.823G>A (p.Ala275Thr)

Heterozygous

0.070105

Disease:	Carnitine palmitoyltransferase I deficiency
Inheritance:	recessive
Significance:	causal
Evidence:	contradicted
Clinvar records:	Benign: not specified Pathogenic: Carnitine palmitoyltransferase I deficiency
Notes:	An entry in ClinVar from GeneReviews reports this causes Carnitine palmitoyltransferase I deficiency, but the corresponding GeneReviews page doesn't list this variant as causal. This variant is very common (contradicting a serious disease effect), and two other labs (GeneDx and Emory Genetics Lab) report this is benign.

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chr3:g.45814094G>A

ClinVar: NM_020208.3(SLC6A20): c.596C>T (p.Thr199Met)

Heterozygous

0.071618

Clinvar entries without associated notes:

Pathogenic: Iminoglycinuria, digenic
Conflicting interpretations of pathogenicity: Hyperglycinuria

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chr8:g.143994266A>G

ClinVar: NM_000498.3(CYP11B2): c.1157T>C (p.Val386Ala)

Homozygous

0.088694

Disease:	Corticosterone methyloxidase deficiency
Inheritance:	recessive
Significance:	causal
Evidence:	contradicted
Clinvar records:	Pathogenic: Corticosterone methyloxidase type 2 deficiency Pathogenic: Corticosterone methyloxidase type 1 deficiency
Notes:	Reported by Pascoe et al., 1992 to cause corticosterone methyloxidase deficiency in a recessive manner, but only when combined with another variant (R181W). Portrat-Doyen et al., 1997 also reported this as a recessive cause in a single family, when homozygous and combined with a different variant (E198D). This variant is extremely common (around 1 in 100 people are homozygous). This is far more common than the rare disease, and it's likely this variant was merely coincidentally present in the cases reported. No other ClinVar submissions or recent literature indicates the variant causes disease. The proposed effect should probably be considered contradicted.

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Clinvar entries without associated notes:

Benign: Corticosterone methyloxidase type 1 deficiency
Benign: Hyperaldosteronism, familial, type I (HALD1)
Benign: Corticosterone methyloxidase type 2 deficiency

chr1:g.98165091T>C

ClinVar: NM_000110.3(DPYD): c.496A>G (p.Met166Val)

Heterozygous

0.089972

Trait:	Toxicity/adverse response to fluorouracil and capecitabine
Inheritance:	other/unknown
Significance:	causal
Evidence:	reported
Clinvar records:	drug response: fluorouracil response - Toxicity/ADR
Notes:	This variant is reported to affect drug metabolism, and is associated with adverse reactions to chemotherapy with fluorouracil and capecitabine.

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Clinvar entries without associated notes:

drug response: capecitabine response - Toxicity/ADR
Likely benign: Dihydropyrimidine dehydrogenase deficiency
not provided: not provided
Benign: not specified

chr1:g.115236057G>A

ClinVar: NM_000036.2(AMPD1): c.133C>T (p.Gln45Ter)

Heterozygous

0.095556

Disease:	Adenosine Deaminase Deficiency
Inheritance:	recessive
Significance:	causal
Evidence:	reported
Clinvar records:	Uncertain significance: Muscle AMP deaminase deficiency (MMDD) Uncertain significance: not provided
Notes:	Reported to cause Adenosine Deaminase Deficiency in a recessive manner. Most of the time individuals do not report symptoms, but when symptoms do exist they to be post-exercise symptoms of muscle weakness, muscle pain, and getting tired more quickly.

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chr8:g.11614575A>G

ClinVar: NM_002052.4(GATA4): c.1129A>G (p.Ser377Gly)

Heterozygous

0.106026

Disease:	Congenital heart defects
Inheritance:	dominant
Significance:	causal
Evidence:	contradicted
Clinvar records:	Benign: not specified Likely pathogenic: not provided
Notes:	One lab reports this as "pathogenic" in ClinVar, but gave no description of the putative disease it causes. OMIM describes other variants in this gene as causing congenital heart defects in a dominant manner. However, if this effect was what their report referred to, it is strongly contradicted by allele frequency – about one in five individuals carries this variant.

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chr12:g.69824024C>T

ClinVar: NC_000012.12: g.69430244C>T

Heterozygous

0.120968

Disease:
Inheritance:	other/unknown
Significance:	causal
Evidence:	reported
Notes:

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Clinvar entries without associated notes:

drug response: hydrochlorothiazide response - Efficacy

chr2:g.63131731G>A

ClinVar: NM_001142615.2(EHBP1): c.1185+30064G>A

Heterozygous

0.122239

Disease:	Prostate cancer
Inheritance:	additive
Significance:	risk factor
Evidence:	reported
Clinvar records:	Pathogenic: Prostate cancer, hereditary, 12 (HPC12)
Notes:	A genome-wide association study by Gudmundsson, et al. 2008 found this variant associated with increased prostate cancer risk in their population (potentially representing an increased lifetime risk of 1 to 2%). Other publications have also examined this variant's association with prostate cancer. A meta-analysis that combined these data by Ao et al. 2015 concluded there was strong evidence for an increased risk association. Most studies did not segregate the effect in heterozygous vs homozygous individuals, but Gudmundsson et al.'s report seemed to indicate the effect is additive.

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chr17:g.4836381C>T

ClinVar: NM_000173.6(GP1BA): c.482C>T (p.Thr161Met)

Heterozygous

0.122947

Clinvar entries without associated notes:

drug response: aspirin response - Efficacy
Benign: not specified

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chr17:g.45360730T>C

ClinVar: NM_000212.2(ITGB3): c.176T>C (p.Leu59Pro)

Heterozygous

0.131786

Disease:	Posttransfusion purpura (PTP)
Inheritance:	recessive
Significance:	risk factor
Evidence:	well-established
Clinvar records:	Benign: PL(A1)/(A2) ALLOANTIGEN POLYMORPHISM :
Notes:	This allele is Pl(A2) in the platelet-specific alloantigen system Pl(A). (The reference genome allele is Pl(A1).) Post-transfusion purpura can occur in women who have been pregnant in the past. It seems to be associated with women who don't carry the PI(A1) variant (e.g. homozygous for this variant), and have developed an immune reaction to Pl(A1) – presumably due to exposure to a fetus carrying a copy of Pl(A1).

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Disease:	Myocardial infarction
Inheritance:	other/unknown
Significance:	risk factor
Evidence:	reported
Clinvar records:	Benign: PL(A1)/(A2) ALLOANTIGEN POLYMORPHISM risk factor: Myocardial infarction
Notes:	Various groups reported that this variant, PIA2, is associated with increased risk of myocardial infarction (heart attack), including Grove et al, 2004 and Zotz et al, 2005. However these reports are all more than a decade old. The lack of replication in follow-up studies may indicate the variant has little or no affect on MI.

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Disease:	Hip fracture
Inheritance:	recessive
Significance:	risk factor
Evidence:	reported
Clinvar records:	Benign: PL(A1)/(A2) ALLOANTIGEN POLYMORPHISM :
Notes:	Tofteng et al. (2007) reported finding an increased risk of hip fractures associated with individuals homozygous for this variant.

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Disease:	Neonatal alloimmune thrombocytopenia
Inheritance:	recessive
Significance:	risk factor
Evidence:	well-established
Clinvar records:	Benign: PL(A1)/(A2) ALLOANTIGEN POLYMORPHISM :
Notes:	This allele is "Pl(A2)" or "HPA-1b" in the platelet-specific alloantigen system. The reference genome allele is "Pl(A1)" or "HPA-1a". Fetuses in mothers who do not have the PI(A1) variant (e.g. homozygous for the this variant) have a risk of neonatal alloimmune thrombocytopenia (also known as NAIT). NAIT can occur when the fetus carries Pl(A1), and the mother does not. An immune response by the mother can cause decreased platelet count in the fetus which can, in turn, cause complications like bleeding, bruising, and intracranial hemorrhage. Peterson et al, 2013 reviews this phenomenon in more detail.

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Clinvar entries without associated notes:

Likely benign: Glanzmann thrombasthenia (GT)
Benign: not specified

chr12:g.21331549T>C

ClinVar: NM_006446.4(SLCO1B1): c.521T>C (p.Val174Ala)

Heterozygous

0.135440

Clinvar entries without associated notes:

drug response: rosuvastatin response - Other
drug response: pravastatin response - Metabolism/PK
drug response: simvastatin response - Toxicity/ADR
drug response: hmg coa reductase inhibitors response - Toxicity/ADR
drug response: cerivastatin response - Toxicity/ADR
Benign: Rotor syndrome (HBLRR)
drug response: hmg coa reductase inhibitors response - Toxicity/ADR, Metabolism/PK
Benign: not specified
drug response: simvastatin acid response - Metabolism/PK
other: not provided

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chr1:g.231408091A>G

ClinVar: NM_014236.3(GNPAT): c.1556A>G (p.Asp519Gly)

Heterozygous

0.144735

Clinvar entries without associated notes:

Pathogenic: Rhizomelic chondrodysplasia punctata type 2 (RCDP2)
Likely benign: Rhizomelic chondrodysplasia punctata (RCDP)
Benign: not provided
Benign: not specified

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chr10:g.96541616G>A

ClinVar: NM_000769.1(CYP2C19): c.681G>A (p.Pro227=)

Heterozygous

0.167273

Clinvar entries without associated notes:

drug response: Mephenytoin, poor metabolism of
drug response: Proguanil, poor metabolism of
drug response: Clopidogrel response
drug response: amitriptyline response - Efficacy
drug response: clopidogrel response - Efficacy, Toxicity/ADR
drug response: citalopram response - Efficacy
drug response: clomipramine response - Efficacy
Likely benign: not specified
other: not provided

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chr4:g.2906707G>T

ClinVar: NM_176801.2(ADD1): c.1378G>T (p.Gly460Trp)

Heterozygous

0.170033

Clinvar entries without associated notes:

risk factor: Hypertension, salt-sensitive essential, susceptibility to
drug response: furosemide and spironolactone response - Efficacy

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chr3:g.124456742G>C

ClinVar: NM_000373.3(UMPS): c.638G>C (p.Gly213Ala)

Heterozygous

0.170189

Clinvar entries without associated notes:

drug response: tegafur response - Toxicity/ADR
drug response: capecitabine response - Toxicity/ADR
drug response: fluorouracil response - Toxicity/ADR
drug response: leucovorin response - Toxicity/ADR
Benign: Orotic aciduria
not provided: not provided
Benign: not specified

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chr16:g.31105554A>C

ClinVar: NM_024006.5(VKORC1): c.173+324T>G

Heterozygous

0.173678

Clinvar entries without associated notes:

drug response: warfarin response - Dosage

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chr10:g.96405502G>A

ClinVar: NC_000010.11: g.94645745G>A

Heterozygous

0.190039

Clinvar entries without associated notes:

drug response: warfarin response - Dosage

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chr20:g.23618427C>T

ClinVar: NM_000099.3(CST3): c.73G>A (p.Ala25Thr)

Heterozygous

0.205317

Disease:	Exudative age-related macular degeneration
Inheritance:	recessive
Significance:	risk factor
Evidence:	reported
Clinvar records:	Pathogenic: Age-related macular degeneration 11 (ARMD11)
Notes:	Reported to be associated with an increased risk of exudative age-related macular degeneration by Butler, et al. 2015 and (Zurdel, et al. 2002)[http://www.ncbi.nlm.nih.gov/pubmed/11815350/). Butler et al. report this effect was only found homozygous individuals, not heterozygous carriers (i.e. in a recessive manner).

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Disease:	Alzheimer's disease
Inheritance:	recessive
Significance:	risk factor
Evidence:	reported
Notes:	Hua et al., 2014 report this has been associated with increased risk of Alzheimer's disease (AD) by a couple different studies. Butler et al., 2015 reported the effect seems to be recessive, only finding homozygous individuals had increased AD risk.

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chr12:g.21382619T>C

ClinVar: NM_006446.4(SLCO1B1): c.1865+4846T>C

Heterozygous

0.211565

Clinvar entries without associated notes:

drug response: methotrexate response - Toxicity/ADR

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chr3:g.38645420T>C

ClinVar: NM_198056.2(SCN5A): c.1673A>G (p.His558Arg)

Heterozygous

0.221139

Clinvar entries without associated notes:

Likely benign: Sick sinus syndrome
Likely benign: Romano-Ward syndrome (RWS)
Likely benign: Dilated Cardiomyopathy, Dominant
Likely benign: Paroxysmal familial ventricular fibrillation
Likely benign: Progressive familial heart block
Pathogenic: Progressive familial heart block type 1A (PFHB1A)
not provided: not provided
Benign: Cardiovascular phenotype
Likely benign: Long QT syndrome (LQTS)
Benign: not specified
Likely benign: Brugada syndrome

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chr14:g.21790040G>T

ClinVar: NM_020366.3(RPGRIP1): c.1639G>T (p.Ala547Ser)

Heterozygous

0.226643

Clinvar entries without associated notes:

Likely benign: Cone-Rod Dystrophy, Recessive
Pathogenic: Cone-rod dystrophy 13 (CORD13)
not provided: not provided
Likely benign: Leber congenital amaurosis (LCA)
Benign: not specified

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chr5:g.179220638A>C

ClinVar: NM_145867.1(LTC4S): c.-444A>C

Heterozygous

0.231208

Clinvar entries without associated notes:

drug response: aspirin response - Toxicity/ADR

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chr16:g.16251599C>T

ClinVar: NM_001171.5(ABCC6): c.3803G>A (p.Arg1268Gln)

Homozygous

0.234689

Disease:	Pseudoxanthoma elasticum (PXE)
Inheritance:	other/unknown
Significance:	causal
Evidence:	contradicted
Clinvar records:	Benign: Pseudoxanthoma elasticum (PXE)
Notes:	Per OMIM 603234.0011, the R1268Q mutation appears in healthy volunteers not affected by PXE, including the homozygous state, at a frequency of 0.19 in an n=62 control group of Caucasians. Frequency in ExAC also contradicts likelihood of a PXE-pathogenic allele.

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Clinvar entries without associated notes:

Likely benign: not provided

chr7:g.142458526A>G

ClinVar: NM_002769.4(PRSS1): c.161A>G (p.Asn54Ser)

Heterozygous

0.242607

Clinvar entries without associated notes:

Pathogenic: Hereditary pancreatitis (PCTT)

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chr10:g.114758349C>T

ClinVar: NM_030756.4(TCF7L2): c.382-41435C>T

Heterozygous

0.254192

Clinvar entries without associated notes:

risk factor: Diabetes mellitus type 2 (NIDDM)
drug response: sulfonamides, urea derivatives response - Efficacy

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chr15:g.78894339G>A

ClinVar: NM_001166694.1(CHRNA3): c.645C>T (p.Tyr215=)

Homozygous

0.255432

Clinvar entries without associated notes:

risk factor: Lung cancer susceptibility 2 (LNCR2)
risk factor: Smoking as a quantitative trait locus 3 (SQTL3)
drug response: nicotine response - Toxicity/ADR

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chr11:g.113270828G>A

ClinVar: NM_178510.1(ANKK1): c.2137G>A (p.Glu713Lys)

Heterozygous

0.258592

Clinvar entries without associated notes:

Benign: Dopamine receptor d2, reduced brain density of
drug response: ethanol response - Toxicity/ADR
drug response: clozapine response - Toxicity/ADR
drug response: olanzapine response - Toxicity/ADR
drug response: antipsychotics response - Toxicity/ADR
drug response: risperidone response - Toxicity/ADR
drug response: bupropion response - Efficacy
Benign: not specified

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chr1:g.11854476T>G

ClinVar: NM_005957.4(MTHFR): c.1286A>C (p.Glu429Ala)

Heterozygous

0.258962

Trait:	MTHFR deficiency risk for elevated homocysteine levels
Inheritance:	other/unknown
Significance:	causal
Evidence:	reported
Clinvar records:	Benign: MTHFR deficiency, thermolabile type
Notes:	Treatment Outcome in support of cause /effect relationship : (Prior to any supplementation) my blood test showed a homocysteine level at 10 (reference range 0 to 15 =normal). So it was still within normal range, however, choosing to attempt to reduce this further, I began to supplement with methylfolate and reduced glutathione sublingual spray (once per day) and successfully significantly lowered my homocysteine level (current range with supplementation has been lowered to between 0 and 2).

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Disease:	neural tube defects in offspring
Inheritance:	other/unknown
Significance:	risk factor
Evidence:	contradicted
Clinvar records:	Likely benign: Neural tube defects, folate-sensitive (NTDFS)
Notes:	User report: successful pregnancy (no folate or folic acid supplementation / low dietary folate intake/ no folic acid fortified foods/ limited natural folate sources) with no neural tube defects of the fetus. (effect was not observed), other contributory factors may be necessary (in combination with this SNP) to produce neural tube defects under low folate levels.

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Clinvar entries without associated notes:

risk factor: Schizophrenia, susceptibility to
Benign: not specified
other: not provided
Uncertain significance: Gastrointestinal stroma tumor (GIST)

chr19:g.41512841G>T

ClinVar: NM_000767.4(CYP2B6): c.516G>T (p.Gln172His)

Heterozygous

0.262184

Clinvar entries without associated notes:

drug response: Efavirenz response
drug response: nevirapine response - Other
drug response: efavirenz response - Dosage
drug response: methadone response - Dosage
drug response: efavirenz response - Toxicity/ADR

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chr7:g.142458451A>T

ClinVar: NM_002769.4(PRSS1): c.86A>T (p.Asn29Ile)

Heterozygous

0.267577

Clinvar entries without associated notes:

Pathogenic: not specified
Pathogenic: Hereditary pancreatitis (PCTT)

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chr19:g.41515263A>G

ClinVar: NM_000767.4(CYP2B6): c.785A>G (p.Lys262Arg)

Homozygous

0.269487

Trait:	Reduced efavirenz metabolism
Inheritance:	additive
Significance:	causal
Evidence:	reported
Clinvar records:	Benign: Efavirenz response
Notes:	Reported by Hass et al, 2004 as associated with reduced metabolism of the drug efavirenz (used to treat HIV), one of several drugs known to be metabolized by this gene's protein product.

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Clinvar entries without associated notes:

drug response: efavirenz response - Metabolism/PK

chr18:g.55247454G>A

ClinVar: NM_001012515.2(FECH): c.68-23C>T

Heterozygous

0.271497

Clinvar entries without associated notes:

Pathogenic: Erythropoietic protoporphyria (EPP1)
Likely benign:

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chr8:g.139884509C>T

ClinVar: NM_152888.2(COL22A1): c.658+5484G>A

Heterozygous

0.273939

Clinvar entries without associated notes:

drug response: salbutamol response - Efficacy

Add effect notes to GenNotes

chr17:g.32579788A>G

ClinVar: NG_012123.1: g.2493A>G

Heterozygous

0.281927

Clinvar entries without associated notes:

risk factor: Spina bifida, susceptibility to
risk factor: Coronary artery disease, modifier of
Pathogenic: Coronary artery disease, development of, in hiv
risk factor: Mycobacterium tuberculosis, susceptibility to

Add effect notes to GenNotes

chr4:g.21391194G>A

ClinVar: NM_025221.5(KCNIP4): c.62-506862C>T

Heterozygous

0.293898

Clinvar entries without associated notes:

drug response: Ace Inhibitors, Plain response - Toxicity/ADR

Add effect notes to GenNotes

chr10:g.104897985T>C

ClinVar: NM_012229.4(NT5C2): c.175+1178A>G

Heterozygous

0.294160

Clinvar entries without associated notes:

drug response: gemcitabine response - Other

Add effect notes to GenNotes

chr19:g.13007458C>T

ClinVar: NM_000159.3(GCDH): c.852+223C>T

Heterozygous

0.298031

Clinvar entries without associated notes:

Likely pathogenic: Glutaric aciduria, type 1 (GA1)

Add effect notes to GenNotes

chr15:g.45673029T>C

ClinVar: NM_001321015.1(GATM): c.-396-270A>G

Heterozygous

0.316521

Clinvar entries without associated notes:

drug response: simvastatin response - Toxicity/ADR
drug response: hmg coa reductase inhibitors response - Toxicity/ADR

Add effect notes to GenNotes

chr19:g.13010643G>T

ClinVar: NM_000159.3(GCDH): c.*288G>T

Heterozygous

0.321357

Clinvar entries without associated notes:

Benign: Glutaric acidemia
Likely pathogenic: Glutaric aciduria, type 1 (GA1)

Add effect notes to GenNotes

chr18:g.55816791G>A

ClinVar: NM_001144968.1(NEDD4L): c.24G>A (p.Gln8=)

Heterozygous

0.322414

Clinvar entries without associated notes:

drug response: hydrochlorothiazide response - Efficacy
drug response: diuretics response - Efficacy

Add effect notes to GenNotes

chr1:g.161514542A>C

ClinVar: NM_001127593.1(FCGR3A): c.526T>G (p.Phe176Val)

Heterozygous

0.324299

Clinvar entries without associated notes:

drug response: rituximab response - Efficacy
drug response: cetuximab response - Efficacy
drug response: trastuzumab response - Efficacy
Likely benign: not specified

Add effect notes to GenNotes

chr16:g.31107689C>T

ClinVar: NM_024006.4(VKORC1): c.-1639G>A

Heterozygous

0.326433

Clinvar entries without associated notes:

Likely benign: not specified
drug response: Warfarin response
other: not provided

Add effect notes to GenNotes

chr16:g.31104878G>A

ClinVar: NM_024006.5(VKORC1): c.174-136C>T

Heterozygous

0.326777

Clinvar entries without associated notes:

drug response: warfarin response - Dosage
drug response: acenocoumarol response - Dosage
drug response: phenprocoumon response - Dosage
Benign: Vitamin K-Dependent Clotting Factors
Likely benign: not specified
drug response: Warfarin response

Add effect notes to GenNotes

chr6:g.151936677G>A

ClinVar: NM_025059.3(CCDC170): c.1810G>A (p.Val604Ile)

Heterozygous

0.341974

Clinvar entries without associated notes:

Likely pathogenic: Estrogen resistance (ESTRR)

Add effect notes to GenNotes

chr9:g.136301982C>G

ClinVar: NM_139025.4(ADAMTS13): c.1342C>G (p.Gln448Glu)

Heterozygous

0.343880

Clinvar entries without associated notes:

Pathogenic: Upshaw-Schulman syndrome (TTP)
Benign: Upshaw-Schulman syndrome (TTP)
Benign: not specified

Add effect notes to GenNotes

chr16:g.57005479C>A

ClinVar: NM_000078.2(CETP): c.658+186C>A

Homozygous

0.346064

Clinvar entries without associated notes:

drug response: HMG CoA reductase inhibitors response - Efficacy

Add effect notes to GenNotes

chr2:g.208494234T>C

ClinVar: NC_000002.12: g.207629510T>C

Heterozygous

0.353666

Clinvar entries without associated notes:

drug response: meperidine response - Dosage
drug response: pentazocine response - Dosage
drug response: morphine response - Dosage
drug response: buprenorphine response - Dosage
drug response: fentanyl response - Dosage
drug response: opioids response - Dosage

Add effect notes to GenNotes

chr11:g.67352689A>G

ClinVar: NM_000852.3(GSTP1): c.313A>G (p.Ile105Val)

Heterozygous

0.353742

Clinvar entries without associated notes:

drug response: fluorouracil and oxaliplatin response - Efficacy
drug response: cyclophosphamide and epirubicin response - Efficacy, Toxicity/ADR
drug response: Platinum compounds response - Toxicity/ADR
drug response: cisplatin response - Toxicity/ADR
not provided: Neoplasm of the large intestine

Add effect notes to GenNotes

chr2:g.234668570C>T

ClinVar: NM_000463.2(UGT1A1): c.-364C>T

Homozygous

0.364805

Clinvar entries without associated notes:

drug response: atazanavir response - Other

Add effect notes to GenNotes

chr16:g.31104509C>G

ClinVar: NM_024006.5(VKORC1): c.283+124G>C

Heterozygous

0.375822

Clinvar entries without associated notes:

drug response: warfarin response - Dosage
Likely benign: not specified

Add effect notes to GenNotes

chr19:g.39738787C>T

ClinVar: NM_001276254.2(IFNL4): c.151-152G>A

Heterozygous

0.377509

Clinvar entries without associated notes:

drug response: peginterferon alfa-2a, peginterferon alfa-2b, ribavirin, and telaprevir response - Efficacy
drug response: peginterferon alfa-2a, peginterferon alfa-2b, and ribavirin response - Efficacy
drug response: peginterferon alfa-2b response - Efficacy
drug response: ribavirin response - Efficacy
drug response: boceprevir response - Efficacy
Benign: not specified

Add effect notes to GenNotes

chr8:g.18257854T>C

ClinVar: NM_000015.2(NAT2): c.341T>C (p.Ile114Thr)

Heterozygous

0.382689

Clinvar entries without associated notes:

drug response: Slow acetylator due to N-acetyltransferase enzyme variant

Add effect notes to GenNotes

chr21:g.37518706G>A

ClinVar: NM_001236.3(CBR3): c.730G>A (p.Val244Met)

Heterozygous

0.383569

Clinvar entries without associated notes:

drug response: anthracyclines and related substances response - Toxicity/ADR

Add effect notes to GenNotes

chr7:g.30726777A>T

ClinVar: NM_001202481.1(CRHR2): c.-166-546T>A

Heterozygous

0.383621

Clinvar entries without associated notes:

drug response: salbutamol response - Efficacy
drug response: selective beta-2-adrenoreceptor agonists response - Efficacy

Add effect notes to GenNotes

chr6:g.151948366G>A

ClinVar: NC_000006.12: g.151627231G>A

Heterozygous

0.392126

Clinvar entries without associated notes:

Likely pathogenic: Estrogen resistance (ESTRR)

Add effect notes to GenNotes

chr16:g.31102321C>T

ClinVar: NM_024006.5(VKORC1): c.*134G>A

Heterozygous

0.394750

Clinvar entries without associated notes:

drug response: phenprocoumon response - Dosage
drug response: warfarin response - Dosage
drug response: acenocoumarol response - Dosage
Benign: Vitamin K-Dependent Clotting Factors

Add effect notes to GenNotes

chr5:g.148206440G>A

ClinVar: NM_000024.5(ADRB2): c.46A= (p.Arg16=)

Heterozygous

0.427364

Clinvar entries without associated notes:

drug response: salbutamol response - Efficacy
drug response: salmeterol response - Efficacy

Add effect notes to GenNotes

chr15:g.45620985C>T

ClinVar: NC_000015.10: g.45328787C>T

Heterozygous

0.429155

Clinvar entries without associated notes:

drug response: hmg coa reductase inhibitors response - Toxicity/ADR
drug response: simvastatin response - Toxicity/ADR

Add effect notes to GenNotes

chr12:g.6954875C>T

ClinVar: NM_002075.3(GNB3): c.825C>T (p.Ser275=)

Heterozygous

0.430953

Clinvar entries without associated notes:

drug response: sildenafil response - Efficacy

Add effect notes to GenNotes

chr7:g.141673345C>G

ClinVar: NM_176817.4(TAS2R38): c.145G>C (p.Ala49Pro)

Homozygous

0.433826

Clinvar entries without associated notes:

drug response: Phenylthiocarbamide tasting

Add effect notes to GenNotes

chr16:g.27356203A>G

ClinVar: NM_000418.3(IL4R): c.223A>G (p.Ile75Val)

Heterozygous

0.446704

Clinvar entries without associated notes:

protective: Atopy, resistance to
Pathogenic: Acquired immunodeficiency syndrome, slow progression to

Add effect notes to GenNotes

chr22:g.19951271G>A

ClinVar: NM_000754.3(COMT): c.472G>A (p.Val158Met)

Heterozygous

0.447522

Clinvar entries without associated notes:

Benign: CATECHOL-O-METHYLTRANSFERASE POLYMORPHISM
drug response: nicotine response - Efficacy
Benign: not specified

Add effect notes to GenNotes

chr11:g.120663363T>C

ClinVar: NM_014619.4(GRIK4): c.83-10039T>C

Homozygous

0.455166

Clinvar entries without associated notes:

drug response: antidepressants response - Efficacy
Benign: not specified

Add effect notes to GenNotes

chr7:g.141672604T>C

ClinVar: NM_176817.4(TAS2R38): c.886A>G (p.Ile296Val)

Homozygous

0.460580

Clinvar entries without associated notes:

drug response: Phenylthiocarbamide tasting

Add effect notes to GenNotes

chr5:g.7870973A>G

ClinVar: NM_002454.2(MTRR): c.66A>G (p.Ile22Met)

Homozygous

0.460708

Clinvar entries without associated notes:

risk factor: Neural tube defects, folate-sensitive, susceptibility to
risk factor: Down syndrome, susceptibility to
drug response: methotrexate response - Toxicity/ADR
Benign: Disorders of Intracellular Cobalamin Metabolism
Uncertain significance: Gastrointestinal stroma tumor (GIST)
Benign: not specified

Add effect notes to GenNotes

chr6:g.160113872A>G

ClinVar: NM_001024465.2(SOD2): c.47T>C (p.Val16Ala)

Heterozygous

0.467640

Clinvar entries without associated notes:

Benign: SUPEROXIDE DISMUTASE 2 POLYMORPHISM
risk factor: Microvascular complications of diabetes 6 (MVCD6)
drug response: cyclophosphamide response - Efficacy

Add effect notes to GenNotes

chr11:g.108283161C>A

ClinVar: NM_152587.3(C11orf65): c.175-5285G>T

Heterozygous

0.482490

Clinvar entries without associated notes:

drug response: metformin response - Efficacy

Add effect notes to GenNotes

chr5:g.63258565C>G

ClinVar: NM_000524.3(HTR1A): c.-1019G>C

Heterozygous

0.487053

Clinvar entries without associated notes:

drug response: paroxetine response - Efficacy
Likely benign: not specified

Add effect notes to GenNotes

chr2:g.49191041C>T

ClinVar: NM_000145.3(FSHR): c.919G>A (p.Ala307Thr)

Heterozygous

0.488321

Clinvar entries without associated notes:

drug response: Ovarian response to FSH stimulation
Benign: Ovarian Dysgenesis
Benign: Ovarian hyperstimulation syndrome (OHSS)
Benign: not specified

Add effect notes to GenNotes

chr6:g.39325078A>G

ClinVar: NM_145027.5(KIF6): c.2155T>C (p.Trp719Arg)

Heterozygous

0.489803

Clinvar entries without associated notes:

drug response: atorvastatin response - Efficacy
drug response: pravastatin response - Efficacy

Add effect notes to GenNotes

chr2:g.166909544C>T

ClinVar: NM_006920.4(SCN1A): c.603-91G>A

Homozygous

0.492283

Clinvar entries without associated notes:

risk factor: Febrile seizures, familial, 3a (FEB3A)
drug response: carbamazepine response - Dosage
drug response: phenytoin response - Dosage
drug response: carbamazepine response - Efficacy
drug response: antiepileptics response - Efficacy

Add effect notes to GenNotes

chr2:g.38298203C>G

ClinVar: NM_000104.3(CYP1B1): c.1294C= (p.Leu432=)

Heterozygous

0.502491

Clinvar entries without associated notes:

drug response: paclitaxel response - Efficacy
drug response: docetaxel response - Efficacy
Benign: not specified

Add effect notes to GenNotes

chr11:g.103418158A>G

ClinVar: NC_000011.10: g.103547430A>G

Heterozygous

0.504150

Clinvar entries without associated notes:

drug response: etoposide response - Toxicity/ADR
drug response: Platinum compounds response - Toxicity/ADR

Add effect notes to GenNotes

chr11:g.18290859C>T

ClinVar: NM_000331.5(SAA1): c.209C>T (p.Ala70Val)

Heterozygous

0.546372

Clinvar entries without associated notes:

Pathogenic: Serum amyloid a variant

Add effect notes to GenNotes

chr16:g.31110981G>A

ClinVar: NG_011564.1: g.296C>T

Heterozygous

0.574455

Clinvar entries without associated notes:

drug response: warfarin response - Dosage

Add effect notes to GenNotes

chr2:g.49189921C>T

ClinVar: NM_000145.3(FSHR): c.2039G>A (p.Ser680Asn)

Heterozygous

0.574874

Clinvar entries without associated notes:

drug response: Ovarian response to FSH stimulation
Benign: Ovarian Dysgenesis
Benign, risk factor: Ovarian hyperstimulation syndrome (OHSS)
Benign: not specified

Add effect notes to GenNotes

chr4:g.187158034G>A

ClinVar: NM_000892.4(KLKB1): c.428G>A (p.Ser143Asn)

Heterozygous

0.600622

Clinvar entries without associated notes:

Pathogenic: Prekallikrein deficiency

Add effect notes to GenNotes

chr7:g.154072020T>C

ClinVar: NM_001039350.2(DPP6): c.52-71279T>C

Heterozygous

0.612054

Clinvar entries without associated notes:

drug response: antipsychotics response - Toxicity/ADR

Add effect notes to GenNotes

chr17:g.7579472G>C

ClinVar: NM_000546.5(TP53): c.215C>G (p.Pro72Arg)

Heterozygous

0.619355

Clinvar entries without associated notes:

Benign: CODON 72 POLYMORPHISM, (rs1042522)
drug response: paclitaxel response - Efficacy, Toxicity/ADR
drug response: cyclophosphamide response - Efficacy, Toxicity/ADR
drug response: antineoplastic agents response - Efficacy, Toxicity/ADR
drug response: fluorouracil response - Efficacy, Toxicity/ADR
drug response: cisplatin response - Efficacy, Toxicity/ADR
Benign: Li-Fraumeni syndrome (LFS)
Benign: Li-Fraumeni syndrome 1 (LFS)
Benign: not provided
Benign: not specified
Benign: Hereditary cancer-predisposing syndrome

Add effect notes to GenNotes

chr4:g.84192168G>C

ClinVar: NM_015697.7(COQ2): c.779-1022C>G

Heterozygous

0.628732

Clinvar entries without associated notes:

drug response: rosuvastatin response - Toxicity/ADR
drug response: atorvastatin response - Toxicity/ADR
drug response: hmg coa reductase inhibitors response - Toxicity/ADR

Add effect notes to GenNotes

chr4:g.6295693C>G

ClinVar: NM_006005.3(WFS1): c.713-1075C>G

Heterozygous

0.630025

Clinvar entries without associated notes:

Pathogenic: Diabetes mellitus, noninsulin-dependent, association with

Add effect notes to GenNotes

chr19:g.13010520A>G

ClinVar: NM_000159.3(GCDH): c.*165A>G

Heterozygous

0.631073

Clinvar entries without associated notes:

Benign: Glutaric acidemia
Likely pathogenic: Glutaric aciduria, type 1 (GA1)

Add effect notes to GenNotes

chr8:g.69389217C>G

ClinVar: NM_052958.3(C8orf34): c.736+8162C>G

Heterozygous

0.637085

Clinvar entries without associated notes:

drug response: irinotecan response - Toxicity/ADR

Add effect notes to GenNotes

chr2:g.60720246C>T

ClinVar: NM_018014.3(BCL11A): c.386-24278G>A

Homozygous

0.639634

Clinvar entries without associated notes:

Likely pathogenic: Fetal hemoglobin quantitative trait locus 5 (HBFQTL5)

Add effect notes to GenNotes

chr16:g.31103796A>G

ClinVar: NM_024006.5(VKORC1): c.283+837T>C

Heterozygous

0.642200

Clinvar entries without associated notes:

drug response: warfarin response - Dosage

Add effect notes to GenNotes

chr3:g.14187449G>T

ClinVar: NM_004628.4(XPC): c.2815C>A (p.Gln939Lys)

Homozygous

0.655551

Clinvar entries without associated notes:

drug response: cisplatin response - Toxicity/ADR
Benign: Xeroderma pigmentosum (XP)
Likely benign: Arrhythmogenic right ventricular cardiomyopathy (ARVD)
Benign: not specified

Add effect notes to GenNotes

chr13:g.47411985A>G

ClinVar: NM_000621.4(HTR2A): c.614-2211T>C

Homozygous

0.655894

Clinvar entries without associated notes:

drug response: Major depressive disorder, response to citalopram therapy in
drug response: antidepressants response - Efficacy
drug response: Selective serotonin reuptake inhibitors response - Efficacy
drug response: citalopram response - Efficacy
Benign: not specified

Add effect notes to GenNotes

chr19:g.41515702T>C

ClinVar: NM_000767.4(CYP2B6): c.823-197T>C

Heterozygous

0.665824

Clinvar entries without associated notes:

drug response: efavirenz response - Metabolism/PK

Add effect notes to GenNotes

chr5:g.35861068T>C

ClinVar: NM_002185.3(IL7R): c.197T>C (p.Ile66Thr)

Homozygous

0.684320

Clinvar entries without associated notes:

Pathogenic: Severe combined immunodeficiency, autosomal recessive, T cell-negative, B cell-positive, NK cell-positive
Benign: not specified
Benign: Severe Combined Immune Deficiency

Add effect notes to GenNotes

chr11:g.17409572T>C

ClinVar: NM_000525.3(KCNJ11): c.67A>G (p.Lys23Glu)

Homozygous

0.708101

Clinvar entries without associated notes:

risk factor: Diabetes mellitus type 2 (NIDDM)
drug response: Exercise stress response, impaired, association with
Benign/Likely benign: Transient Neonatal Diabetes, Dominant
Benign/Likely benign: Hyperinsulinism, Dominant/Recessive
Likely benign: Maturity onset diabetes mellitus in young (MODY)
Benign: Islet cell hyperplasia (HHF2)
Benign: Permanent neonatal diabetes mellitus (PNDM)
Benign: not specified

Add effect notes to GenNotes

chr19:g.44055726T>C

ClinVar: NM_006297.2(XRCC1): c.1196A>G (p.Gln399Arg)

Homozygous

0.719960

Clinvar entries without associated notes:

drug response: carboplatin response - Efficacy
drug response: cisplatin response - Efficacy
drug response: oxaliplatin response - Efficacy
drug response: platinum response - Efficacy
drug response: Platinum compounds response - Efficacy

Add effect notes to GenNotes

chr5:g.35871190G>A

ClinVar: NM_002185.3(IL7R): c.412G>A (p.Val138Ile)

Homozygous

0.725215

Clinvar entries without associated notes:

Pathogenic: Severe combined immunodeficiency, autosomal recessive, T cell-negative, B cell-positive, NK cell-positive
Benign: not specified
Benign: Severe Combined Immune Deficiency

Add effect notes to GenNotes

chr1:g.78956432T>C

ClinVar: NM_000959.3(PTGFR): c.-562T>C

Heterozygous

0.764567

Clinvar entries without associated notes:

drug response: latanoprost response - Efficacy

Add effect notes to GenNotes

chr6:g.35669983A>G

ClinVar: NM_001145775.2(FKBP5): c.-20+18122T>C

Heterozygous

0.769253

Clinvar entries without associated notes:

drug response: fluoxetine response - Efficacy
drug response: Selective serotonin reuptake inhibitors response - Efficacy
drug response: mirtazapine response - Efficacy
drug response: antidepressants response - Efficacy
drug response: venlafaxine response - Efficacy
drug response: paroxetine response - Efficacy
drug response: citalopram response - Efficacy

Add effect notes to GenNotes

chr7:g.99382096C>T

ClinVar: NM_017460.5(CYP3A4): c.-392G>A

Homozygous

0.791650

Clinvar entries without associated notes:

Benign: CYP3A4 PROMOTER POLYMORPHISM
Benign: Cyp3a4-v
drug response: tacrolimus response - Dosage

Add effect notes to GenNotes

chr13:g.95714976C>T

ClinVar: NM_005845.4(ABCC4): c.3348G>A (p.Lys1116=)

Homozygous

0.796717

Clinvar entries without associated notes:

drug response: tenofovir response -
drug response: tenofovir response - Metabolism/PK

Add effect notes to GenNotes

chr1:g.169519049T>C

ClinVar: NM_000130.4(F5): c.1601G= (p.Arg534=)

Homozygous

0.983048

Clinvar entries without associated notes:

drug response: hormonal contraceptives for systemic use response - Toxicity/ADR
Pathogenic: not provided

Add effect notes to GenNotes