hu7AC640 (23&me) - GET-Evidence variant report

Variant report for hu7AC640 (23&me)

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VariantClinical
Importance
ImpactAllele
freq
Summary
1UGT1A1-G71RModerateLikelyLikely pathogenic

Complex/Other, Heterozygous
0.000743632This variant, also known as UGT1A1*6, is associated with Gilbert syndrome (found in ~5% of the population) and transient hyperbilirubinemia in infants in east asian populations. This allele appears to have incomplete penetrance and causes reduced enzyme activity.1
2MEFV-E148QModerateUncertainUncertain pathogenic

Recessive, Homozygous
0.0120929Some reports believe this cause Familial Mediterranean Fever in a recessive manner with reduced penetrance (i.e. not all get the disease). However, these reports lack strong statistical significance; other studies argue the variant is not associated with the disease.1
3H6PD-R453QLowUncertainUncertain pathogenic

Recessive, Homozygous
0.308886This common variant may have a small pathogenic effect by contributing to cortisone reductase deficiency (a rare abnormality) when homozygous and combined with a serious pathogenic variant. The same authors have tested and ruled out a contribution to polycystic ovary syndrome (similar phenotype, more common disease).1
4SP110-L425SLowUncertainUncertain pathogenic

Unknown, Homozygous
0.863357This variant is associated with a slightly increased risk of tuberculosis. It is unclear whether it is itself causal, or in linkage disequilibrium with some other causal variant that has a stronger effect.1
5BRCA2-N372HLowUncertainUncertain pathogenic

Recessive, Carrier (Heterozygous)
0.23656This is a common variant of BRCA2 (HapMap allele frequency of 23%). The variant is weakly associated with an increased chance of breast cancer, and zygosity of the variant is associated with sex of children: male children are more likely to be homozygous for this variant, female children are more likely to be heterozygous.1
6TP53-P72RLowUncertainUncertain pathogenic

Unknown, Heterozygous
0.627743This is a common variant was first reported as a polymorphism. It has since had mixed associations with cancer: Storey et al. conclude a 7x *increased* risk of HPV cancer for homozygotes vs hets, but Jones et al. find a 1.98x *decreased* risk for colorectal cancer. This variant may have significant impact on particular cancers, but it is unclear what effect it has on the overall burden of cancer.1
7WFS1-R611HLowUncertainUncertain not reviewed

Recessive, Carrier (Heterozygous)
0.400446This nonsynonymous SNP is associated with Wolfram Syndrome (known as DIDMOAD), which is characterized by early-onset non-autoimmune diabetes mellitus, diabetes insipidus, optic atrophy, and deafness) and to adult Type Two Diabetes Mellitus. The WFS1 gene maps to chromosome 4p16.3. The variant has been shown to be statistically associated with type II diabetes in six UK studies and one study of Ashkenazi Jews (Sandhu, M., et al., Minton et al.).1
8CFH-V62ILowLikelyLikely protective

Complex/Other, Heterozygous
0.391616Associated with a decreased risk for age related macular degeneration (ARMD). Homozygotes for this have a 4-5% decreased attributable risk (3-4% vs. average 8% risk), heterozygotes have slightly lower than average risk (7%). Non-carriers have an increased risk (12-13%). ARMD impairs sharp vision as age progresses. While there is no cure, treatment can slow progression of the disease and environmental factors (smoking and obesity) contribute to higher risk.1
9KCNJ11-K23ELowLikelyLikely protective

Unknown, Heterozygous
0.738148This variant is associated with decreased risk of type 2 diabetes. It is unclear whether this variant has additive effects, or acts in a dominant or recessive manner. Assuming diabetes has a lifetime risk of 36%, we estimate a decreased risk of around 1-2% per copy of this variant.1
10OCA2-H615RLowLikelyLikely benign

Complex/Other, Heterozygous
0.000650678Associated with lighter skin pigmentation in East Asian populations.1
11PMS2-P470SLowLikelyLikely benign

Unknown, Homozygous
0.374884Benign, common variant.1
12SLC45A2-E272KLowLikelyLikely benign

Unknown, Heterozygous
0.0290946Pigmentation allele for black hair in Caucasian population.1
13TPCN2-G734ELowUncertainUncertain benign

Unknown, Heterozygous
0.286166Pigmentation allele.1
14FMO3-V257MLowUncertainUncertain benign

Unknown, Heterozygous
0.0570738This common variant (HapMap allele frequency of 9.2%) appears to have no functional effect. OMIM has recorded it as having been seen homozygously in an individual with Trimethylaminuria, but Treacy et al. 1998 conclude it is a polymorphism.1
15EDAR-V370ALowUncertainUncertain benign

Unknown, Homozygous
0.0105968Associated with thicker hair, common in Chinese and Japanese individuals and thought to be Asian-specific.1
16APOB-Y1422CLowUncertainUncertain benign

Unknown, Homozygous
0.999628This position is almost certainly an error in the HG18 reference sequence. 1
17TAS2R38-A49PLowUncertainUncertain benign

Unknown, Homozygous
0.431121This variant is strongly associated with causing the "taster" phenotype of phenylthiocarbamine (PTC) in a dominant manner.1
18GFAP-D295NLowUncertainUncertain benign

Unknown, Heterozygous
0.0333767Reported as a nonpathogenic polymorphism.1
19PCSK9-G670ELowUncertainUncertain benign

Unknown, Homozygous
0.888269This variant is likely benign. 1
20PTCH1-P1315LLowUncertainUncertain benign

Unknown, Heterozygous
0.29631Common polymorphism, presumed benign.1
21ABCC11-G180RLowUncertainUncertain benign

Unknown, Homozygous
0.0976947This variant is associated with dry type ear wax (a benign trait) in a recessive manner.1
22TAS2R38-I296VLowUncertainUncertain benign

Unknown, Homozygous
0.463376This variant is associated with "taster" status of PTC, along with 49P and 262A. Due to linkage disequilibrium, the independent effects of positions 296 and 262 is unclear. The presence of 49P confers taster status in a dominant fashion, but in the absence of 49P, the presence of 262A/296V is still positively associated with tasting PTC.1
VariantPrioritization scoreAllele
freq
Num of
articles
Zygosity and Prioritization Score Reasons

Gene search

"GENE" or "GENE A123C":

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