huA27736 (Full Genome 2013) - GET-Evidence variant report

Variant report for huA27736 (Full Genome 2013)

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VariantClinical
Importance
ImpactAllele
freq
Summary
1C3-R102GModerateLikelyLikely pathogenic

Complex/Other, Heterozygous
0.152073This variant (also called C3F) is common in Europeans (10.2% allele frequency), and is associated with age-related macular degeneration. In the US, 1.5% of adults over 40 have the disease, but the incidence increases strongly with age (>15% in women over 80). Assuming an average lifetime risk of ~10%, heterozygous individuals have a ~13% risk and homozygous have ~20%.1
2KRT5-G138ELowLikelyLikely pathogenic

Unknown, Heterozygous
0.0521472This variant is associated with 1.25x increased risk of basal cell carcinoma (common skin cancer, rarely malignant).1
3MTRR-I49MLowLikelyLikely pathogenic

Recessive, Carrier (Heterozygous)
0.451199This common variant (HapMap allele frequency of 31.3%) in a protein involved in folate (B9) and cobalamin (B12) metabolism and is often reported as "MTRR I22M" (an alternative transcript position). Mothers homozygous for this variant are associated with having around a increased chance of a child with Down syndrome (risk of 0.4%, average risk in population is 0.25%). Notably, age plays a far larger role in the rate of Down syndrome (risk is 4.5% for a mother 45-years-of-age), and it is unknown how this variant may combine with the effect of age. There are conflicting reports associating this variant with incidence of neural tube defects, possibly when combined with MTHFR A222V.1
4NOD2-G908RLowLikelyLikely pathogenic

Unknown, Heterozygous
0.0106897This variant is associated with an increased susceptibility to Crohn's disease and other inflammatory bowel diseases (IBD). Assuming an overall prevalence of 0.5% for IBD, this variant implies an increased attributable risk of 2% (5x increased risk, for an overall risk of 2.5% of IBD for people with this variant).1
5rs5186LowLikelyLikely pathogenic

Unknown, Heterozygous
0.214878This common noncoding genetic variant has an allele frequency of ~30% and is associated with an increased risk of hypertension. If ~25% of non-carriers have hypertension, Bonnardeaux et al's data predict ~4% increased risk of hypertension per copy of this variant. This SNP is in the 3' noncoding region of the AGTR1 transcript (angiotensin II type 1 receptor), also known as AT2R1 or AT1R, which is a target of hypertension drugs.1
6LRP5-A1330VLowUncertainUncertain pathogenic

Complex/Other, Heterozygous
0.110367In a study of a UK population this variant was associated with a small increased risk of osteoporosis and osteoporotic bone fractures, with each copy of the variant presumed to have an additive effect. A study in Chinese young men failed to find an association with peak bone density. 1
7TGFB1-R25PLowUncertainUncertain pathogenic

Complex/Other, Heterozygous
0.0488858This variant in a growth factor gene is associated with variation in TGFB1 levels; this has been associated with various pathogenic and some protective effects, including: more hepatic fibrosis progression in hep C patients, lower risk of cleft palate, anticorrelation with longevity, higher risk of myocardial infarction and lower risk of hypertension.1
8SP110-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
9TP53-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
10ABCC6-R1268QLowUncertainUncertain pharmacogenetic

Unknown, Heterozygous
0.218907This common polymorphism appears to not have a significant phenotypic impact. A few studies report weak but significant associations with plasma lipids (in Inuits) and thalidomide toxicity.1
11rs1544410LowUncertainUncertain pharmacogenetic

Unknown, Heterozygous
0.351562rs1544410 is a Vitamin D Receptor (VDR) single nucleotide polymorphism. It is unlikely that it has functional significance because it is located in an intron (Liu et. al.), but it is in strong linkage disequilibrium with rs731236 (Dvornyk et al), which is located in an exon. 1
12FUT2-W154XModerateWell-establishedWell-established protective

Recessive, Carrier (Heterozygous)
0.490519This recessive protective variant confers resistance to norovirus (which causes stomach flu). 20% of Caucasians and Africans are homozygous for this variant and are "non-secretors": they do not express ABO blood type antigens in their saliva or mucosal surfaces. Most strains of norovirus bind to these antigens in the gut, and so this non-secretor status confers almost total resistantance to most types of norovirus. There are notable exceptions, some strains of norovirus bind a different target and are equally infectious for secretors and non-secretors.1
13PCSK9-R46LModerateLikelyLikely protective

Unknown, Heterozygous
0.0101389This variant is reported to have a dominant protective effect against coronary heart disease. Carriers of this variant have about half the risk of coronary heart disease compared to non-carriers (6.3% risk in carriers vs. 11.8% risk in non-carriers).1
14CFH-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
15NPC1-H215RLowLikelyLikely protective

Complex/Other, Homozygous
0.295687This variant is associated with a reduced risk of obesity, with an additive effect of -0.084 BMI per allele (an average of 0.54 pounds less, per allele, in a 5'6" individual). 1
16KCNJ11-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
17MTR-D919GLowUncertainUncertain protective

Complex/Other, Heterozygous
0.217234This variant was weakly associated with a protective effect vs. colorectal cancer, but only in individuals with low alcohol consumption. 1
18LPL-S474XLowUncertainUncertain protective

Unknown, Heterozygous
0.0844953This variant actually increases LPL enzyme activity despite creating a termination codon (see Rip J et al). It appears to be a protective variant, associated with lower triglyceride levels--although the effect is quite weak and explains only 0.5-1% of triglyceride variation.1
19PMS2-P470SLowLikelyLikely benign

Unknown, Homozygous
0.374884Benign, common variant.1
20SLC45A2-E272KLowLikelyLikely benign

Unknown, Heterozygous
0.0290946Pigmentation allele for black hair in Caucasian population.1
21SDHB-S163PLowUncertainUncertain benign

Unknown, Heterozygous
0.0104109We evaluate as uncertain but presumed benign. One report linked this variant to Cowden-like syndromes, but the significance of their findings is unclear and other reports treat this as a non-pathological variation.1
22PCSK9-G670ELowUncertainUncertain benign

Unknown, Homozygous
0.888269This variant is likely benign. 1
23DSPP-R68WLowUncertainUncertain benign

Unknown, Heterozygous
0.143045Probably benign. One report linked this to causing dentinogenesis Imperfecta type II in a large Swedish family, but subsequent publications have observed this is a common variant and conclude it is a nonpathogenic polymorphism.1
24APOB-Y1422CLowUncertainUncertain benign

Unknown, Homozygous
0.999628This position is almost certainly an error in the HG18 reference sequence. 1
25GUCY2D-A52SLowUncertainUncertain benign

Recessive, Carrier (Heterozygous)
0.21016One publication suggested that this variant possibly causes Leber's congenital amaurosis in a recessive manner, but the frequency data (36% in 1000 genomes) contradicts any significant pathogenic effect.1
26RP1-N985YLowUncertainUncertain benign

Unknown, Heterozygous
0.348671Probably benign. One report linked this variant to high triglycerides, but a later paper found a nearby SNP with similar association and suggests that both findings are caused by linkage to an undiscovered causal variant.1
27TAS2R38-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
28SLC45A2-L374FLowUncertainUncertain benign

Unknown, Heterozygous
0.691764Pigmentation allele for non-black hair, and consequently, possible increased susceptibility to malignant melanoma.1
29TAS2R38-A49PLowUncertainUncertain benign

Unknown, Homozygous
0.431121This variant is strongly associated with causing the "taster" phenotype of phenylthiocarbamine (PTC) in a dominant manner.1
VariantPrioritization scoreAllele
freq
Num of
articles
Zygosity and Prioritization Score Reasons

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"GENE" or "GENE A123C":

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