Variant report for hu7379BC (23andMe)
- Data source: hu7379BC (23andMe)
- This report: evidence.pgp-hms.org/genomes?display_genome_id=4eabd0736248111670373c9aa3d03137354d9c9b&access_token=8def298e7da25600768ddbc6ce8994b4
- Download: source data
- Processing status: processing
- Show debugging info
Log file:
| Row number | Variant | Clinical Importance | Evidence | Impact | Allele freq | Summary | Sufficient |
|---|---|---|---|---|---|---|---|
| 1 | 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 |
| 2 | MTRR-I49M | Low | Likely | Likely pathogenic Recessive, Carrier (Heterozygous) | 0.451199 | This 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 |
| 3 | RNASEL-R462Q | Low | Uncertain | Uncertain pathogenic Complex/Other, Homozygous | 0.278026 | Associated with increased risk of prostate cancer in individuals who already have a family history of prostate cancer, but studies have been unable to replicate this finding in sporadic (non-familial) prostate cancer cases. | 1 |
| 4 | ELAC2-S217L | Low | Uncertain | Uncertain pathogenic Complex/Other, Homozygous | 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 | 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 |
| 6 | 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 |
| 7 | TP53-P72R | Low | Uncertain | Uncertain pathogenic Unknown, Heterozygous | 0.627743 | This 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 |
| 8 | 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 |
| 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 | FUT2-W154X | Moderate | Well-established | Well-established protective Recessive, Homozygous | 0.490519 | This 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 |
| 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 | 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 |
| 13 | ARSA-N350S | Low | Well-established | Well-established benign Unknown, Homozygous | 0.183199 | This common variant (HapMap 24.1% allele frequency) causes a loss of a glycosylation site (affecting the size of the protein when studied with gel electrophoresis) but does not affect enzyme activity or stability. | 1 |
| 14 | OCA2-R419Q | Low | Likely | Likely benign Unknown, Heterozygous | 0.0565161 | This variant is associated with eye color, as is OCA2 R305W. Individuals with this variant are reported to be more likely to have green/hazel eyes as opposed to blue/gray eyes. Other variants in this gene are associated with oculocutaneous albinism (albinism which involves skin and eyes). | 1 |
| 15 | MYO7A-R302H | Low | Likely | Likely benign Unknown, Heterozygous | 0.00170487 | Weston, et al. 1996 reported seeing this on the same DNA strand with another variant in a couple cases of Usher Type I syndrome. That other variant was believed to cause disease in a recessive manner, while this variant was speculated to be coincidental observed. ExAC allele frequency data confirms that this variant is merely uncommon in Europeans (1 in 170 are carriers). If it were causal, it would be a well-established cause; the lack of such evidence in the literature confirms that the variant is not a "Mendelian" cause of Usher Type I syndrome. | 1 |
| 16 | PMS2-P470S | Low | Likely | Likely benign Unknown, Heterozygous | 0.374884 | Benign, common variant. | 1 |
| 17 | MLH1-I219V | Low | Uncertain | Uncertain benign Dominant, Heterozygous | 0.239822 | Computational evidence, functional assays, and case/control studies suggest this variant is probably benign. | 1 |
| 18 | FBN2-S2580L | Low | Uncertain | Uncertain benign Dominant, Heterozygous | 0.0779885 | Probably benign -- initially associated with congenital contractual arachnodactyly, but later reports classify it as a nonpathogenic polymorphism. | 1 |
| 19 | LOXL1-R141L | Low | Uncertain | Uncertain benign Complex/Other, Heterozygous | 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 |
| 20 | RPGRIP1-A547S | Low | Uncertain | Uncertain benign Complex/Other, Heterozygous | 0.232202 | Probably benign. Implicated in causing autosomal recessive cone-rod dystrophy, but a later report found the same incidence in controls and concludes it is not causal. | 1 |
| 21 | FANCA-S1088F | Low | Uncertain | Uncertain benign Unknown, Heterozygous | 0.0584681 | Probably benign. One report hypothesized this variant causing Fanconi Anemia, but the allele frequency (3-7%) is high enough to contradict a highly penetrant pathogenic effect. Later authors have concluded this is a polymorphism, not pathogenic. | 1 |
| 22 | PCCA-I475V | Low | Uncertain | Uncertain benign Unknown, Heterozygous | 0.0377394 | Reported as a polymorphism, tentatively presumed benign. | 1 |
| 23 | MUSK-T100M | Low | Uncertain | Uncertain benign Unknown, Heterozygous | 0.023413 | Probably benign. | 1 |
| 24 | TYR-S192Y | Low | Uncertain | Uncertain benign Unknown, Heterozygous | 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 |
| 25 | 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 |
| 26 | APOB-Y1422C | Low | Uncertain | Uncertain benign Unknown, Homozygous | 0.999628 | This position is almost certainly an error in the HG18 reference sequence. | 1 |
| 27 | PCSK9-G670E | Low | Uncertain | Uncertain benign Unknown, Heterozygous | 0.888269 | This variant is likely benign. | 1 |
| 28 | TPCN2-G734E | Low | Uncertain | Uncertain benign Unknown, Heterozygous | 0.286166 | Pigmentation allele. | 1 |
| 29 | PTCH1-P1315L | Low | Uncertain | Uncertain benign Unknown, Homozygous | 0.29631 | Common polymorphism, presumed benign. | 1 |
| Row number | Variant | Prioritization score | Allele freq | Num of articles | Zygosity and Prioritization Score Reasons | Sufficient |
|---|