Variant report for huC170B1 (23+me+DW)
- Data source: huC170B1 (23+me+DW)
- This report: evidence.pgp-hms.org/genomes?display_genome_id=d43c0a9dfef85f81f6ba82b0c5291aff18491ead&access_token=61cfdb75be81651b4acb4fdfbe175f75
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| Row number | Variant | Clinical Importance | Evidence | Impact | Allele freq | Summary | Sufficient |
|---|---|---|---|---|---|---|---|
| 1 | COL4A1-Q1334H | Low | Likely | Likely pathogenic Dominant, Homozygous | 0.324689 | This common variant has been associated with arterial stiffness and, in Japanese, a small increased risk of myocardial infarction (MI, a.k.a. heart attack). This last observation supported a dominant effect for this variant and, assuming a lifetime risk of 15% for MI, we estimate carriers have an additional risk of 0.5-3%. | 1 |
| 2 | rs5186 | Low | Likely | Likely pathogenic Unknown, Heterozygous | 0.214878 | This 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 |
| 3 | MBL2-G54D | Low | Likely | Likely pathogenic Recessive, Carrier (Heterozygous) | 0.103923 | This variant is associated with mannose binding protein deficiency which leads to impaired complement system immune response to mannose-rich pathogens. Patients homozygous for this allele or compound heterozygous are likely to have increased susceptibility to infection, but Hellemann et al. report heterosis for intensive care outcomes in heterozygous subjects. The wild-type version of this gene is known as variant allele A, while this is called variant allele B. See R52C (variant D) and G57E (variant C). | 1 |
| 4 | ELAC2-S217L | Low | Uncertain | Uncertain pathogenic Complex/Other, Heterozygous | 0.273471 | Reported to be associated with increased susceptibility to prostate cancer, but later studies weaken the hypothesis. Xu et al.'s meta-analysis concludes that there is a small but significant increased risk (OR = 1.13). Assuming a lifetime risk of 16% for prostate cancer we calculate this leads to an increased risk of ~1.5% (17.5% total). | 1 |
| 5 | H6PD-R453Q | Low | Uncertain | Uncertain pathogenic Recessive, Carrier (Heterozygous) | 0.308886 | This 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 |
| 6 | SP110-L425S | Low | Uncertain | Uncertain pathogenic Unknown, Homozygous | 0.863357 | This 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 |
| 7 | WFS1-R611H | Low | Uncertain | Uncertain not reviewed Recessive, Carrier (Heterozygous) | 0.400446 | This 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 |
| 8 | ABCC6-R1268Q | Low | Uncertain | Uncertain pharmacogenetic Unknown, Heterozygous | 0.218907 | This 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 |
| 9 | rs1544410 | Low | Uncertain | Uncertain pharmacogenetic Unknown, Homozygous | 0.351562 | rs1544410 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 |
| 10 | NPC1-H215R | Low | Likely | Likely protective Complex/Other, Heterozygous | 0.295687 | This 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 |
| 11 | CFH-V62I | Low | Likely | Likely protective Complex/Other, Heterozygous | 0.391616 | Associated 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 |
| 12 | KCNJ11-K23E | Low | Likely | Likely protective Unknown, Heterozygous | 0.738148 | This 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 |
| 13 | IL7R-T244I | Low | Likely | Likely protective Unknown, Homozygous | 0.210169 | The reference genome variant for this allele has been associated with a slight increased risk of multiple sclerosis. Thus, this variant can be treated as a "protective" variant -- carriers of this variant are slightly less likely to have MS. Because the disease is rare and the effect of this variant is not very strong, the absolute decreased risk for carriers of this variant is less than .05% (less than 1 in 2000). | 1 |
| 14 | DTNBP1-P272S | Low | Uncertain | Uncertain protective Recessive, Carrier (Heterozygous) | 0.0351366 | Possibly a slight protective effect against colorectal cancer if homozygous. | 1 |
| 15 | PMS2-P470S | Low | Likely | Likely benign Unknown, Heterozygous | 0.374884 | Benign, common variant. | 1 |
| 16 | EFHC1-R182H | Low | Likely | Likely benign Unknown, Heterozygous | 0.0439673 | Probably benign. OMIM appears to incorrectly interpret literature as linking this variant to juvenile myoclonic epilepsy; the authors report it as a polymorphism. | 1 |
| 17 | LOXL1-R141L | Low | Uncertain | Uncertain benign Complex/Other, Homozygous | 0.255899 | Associated with exfoliative glaucoma & syndrome (XFG & XFS) in various populations, but with contradicting results (protective in Caucasians, pathogenic in Japanese). Based on this it seems the variation itself -- although it affects protein structure -- is not itself causing disease. Instead it is likely associated with other nearby causal variants. As such, it is evaluated as benign by GET-Evidence (which focuses on reporting causal variants). See detailed variant report for disease risk associations. | 1 |
| 18 | TYR-S192Y | Low | Uncertain | Uncertain benign Unknown, Homozygous | 0.270682 | This variant is reported to affect skin pigmentation. It is associated with lighter skin in South Asians (OR 4-5) and with a lack of freckles in Europeans (OR 1.3). | 1 |
| 19 | PCCA-I475V | Low | Uncertain | Uncertain benign Unknown, Heterozygous | 0.0377394 | Reported as a polymorphism, tentatively presumed benign. | 1 |
| 20 | DSPP-R68W | Low | Uncertain | Uncertain benign Unknown, Homozygous | 0.143045 | Probably 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 |
| 21 | TPCN2-G734E | Low | Uncertain | Uncertain benign Unknown, Homozygous | 0.286166 | Pigmentation allele. | 1 |
| 22 | APOB-Y1422C | Low | Uncertain | Uncertain benign Unknown, Homozygous | 0.999628 | This position is almost certainly an error in the HG18 reference sequence. | 1 |
| 23 | SLC45A2-L374F | Low | Uncertain | Uncertain benign Unknown, Homozygous | 0.691764 | Pigmentation allele for non-black hair, and consequently, possible increased susceptibility to malignant melanoma. | 1 |
| 24 | ABCC11-G180R | Low | Uncertain | Uncertain benign Unknown, Heterozygous | 0.0976947 | This variant is associated with dry type ear wax (a benign trait) in a recessive manner. | 1 |
| 25 | MAPT-R370W | Low | Uncertain | Uncertain benign Unknown, Heterozygous | 0.155549 | Probably benign. | 1 |
| 26 | PCSK9-G670E | Low | Uncertain | Uncertain benign Unknown, Homozygous | 0.888269 | This variant is likely benign. | 1 |
| 27 | PKP2-L366P | Low | Uncertain | Uncertain benign Unknown, Homozygous | 0.221231 | This variant is a benign polymorphism. | 1 |
| 28 | TAS2R38-I296V | Low | Uncertain | Uncertain benign Unknown, Heterozygous | 0.463376 | This 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 |
| 29 | RP1-N985Y | Low | Uncertain | Uncertain benign Unknown, Heterozygous | 0.348671 | Probably 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 |
| 30 | TAS2R38-A49P | Low | Uncertain | Uncertain benign Unknown, Heterozygous | 0.431121 | This variant is strongly associated with causing the "taster" phenotype of phenylthiocarbamine (PTC) in a dominant manner. | 1 |
| Row number | Variant | Prioritization score | Allele freq | Num of articles | Zygosity and Prioritization Score Reasons | Sufficient |
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