Variant report for huB1488D (v.3 platform)
- Data source: huB1488D (v.3 platform)
- This report: evidence.pgp-hms.org/genomes?display_genome_id=417dea0dea81239a2d1d19e24f055dfb74504b38&access_token=a6e005436dc057f849d1ddd3cd84b216
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Log file:
| Row number | Variant | Clinical Importance | Evidence | Impact | Allele freq | Summary | Sufficient |
|---|---|---|---|---|---|---|---|
| 1 | C3-R102G | Moderate | Likely | Likely pathogenic Complex/Other, Heterozygous | 0.152073 | This 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 |
| 2 | PPARG-P12A | Moderate | Uncertain | Uncertain not reviewed Unknown, Heterozygous | 0.0886782 | 1 | |
| 3 | NOD2-R702W | Low | Likely | Likely pathogenic Complex/Other, Heterozygous | 0.0334821 | NOD2 encodes a protein involved in bacterial recognition. This variant is associated with Crohn's disease in European populations, but not in Korean or Japanese groups. | 1 |
| 4 | 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 |
| 5 | AMPD1-Q12X | Low | Likely | Likely pathogenic Recessive, Carrier (Heterozygous) | 0.0930643 | Causes 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. | 1 |
| 6 | WFS1-R611H | Low | Uncertain | Uncertain not reviewed Recessive, Homozygous | 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 | 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 |
| 8 | SP110-L425S | Low | Uncertain | Uncertain pathogenic Unknown, Heterozygous | 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 |
| 9 | 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 |
| 10 | BRCA2-N372H | Low | Uncertain | Uncertain pathogenic Recessive, Carrier (Heterozygous) | 0.23656 | This 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 |
| 11 | TP53-P72R | Low | Uncertain | Uncertain pathogenic Unknown, Homozygous | 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 |
| 12 | ITPA-P32T | Low | Well-established | Well-established pharmacogenetic Recessive, Carrier (Heterozygous) | 0.0609779 | This variant is associated with inosine triphosphate pyrophosphohydrolase deficiency and may be associated with an adverse reaction to thiopurine drugs (which are used as immunosuppressants). Homozygotes have no detectable ITPase activity, individuals compound heterozygous with another less severe mutation also have severely reduced enzyme activity. | 1 |
| 13 | rs1544410 | Low | Uncertain | Uncertain pharmacogenetic Unknown, Heterozygous | 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 |
| 14 | 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 |
| 15 | 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 |
| 16 | IL7R-T244I | Low | Likely | Likely protective Unknown, Heterozygous | 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 |
| 17 | ARSA-N350S | Low | Well-established | Well-established benign Unknown, Heterozygous | 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 |
| 18 | ADA-K80R | Low | Likely | Likely benign Recessive, Carrier (Heterozygous) | 0.0635806 | This variant has a 3.5% allele frequency in 1000 genomes data. Although OMIM links this to disease, the paper they reference uses in vitro data to conclude that this is a functionally neutral polymorphism. | 1 |
| 19 | 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 |
| 20 | KEL-T193M | Low | Uncertain | Uncertain benign Dominant, Heterozygous | 0.0320692 | This variant is also known as Kell or K1 or K (capitalized) in the Kell antigen system. K1-negative mothers (carrying no copies of this variant) carrying K1-positive fetuses (heterozygous or homozygous) are at risk for hemolytic disease of the newborn. About 9% of caucasians carry one or two copies of K1. | 1 |
| 21 | 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 |
| 22 | 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 |
| 23 | ALOX12B-P127S | Low | Uncertain | Uncertain benign Complex/Other, Heterozygous | 0.0167317 | This variant was found heterozygously in autosomal recessive congenital ichthyosis in two Turkish siblings, although the second mutation was not found. Later, Lesueur et al. observe that this variant has a 4% frequency in their North African controls and is likely just a rare SNP. | 1 |
| 24 | CYP27A1-P384L | Low | Uncertain | Uncertain benign Unknown, Heterozygous | 0.0177542 | Probably not pathogenic. Although predicted to be disruptive and treated by some as pathogenic, reports of this variant in cases were all linked with an upstream frameshift variant -- this supports the variant as a nonpathogenic ancestral polymorphism. | 1 |
| 25 | UNC13D-A59T | Low | Uncertain | Uncertain benign Unknown, Heterozygous | 0.0171965 | Probably benign. This variant was reported to cause haemophagocytic lymphohistiocytosis in a recessive manner, but its allele frequency is inconsistent with this hypothesis and so we evaluate it as a nonpathogenic polymorphism. | 1 |
| 26 | TPCN2-G734E | Low | Uncertain | Uncertain benign Unknown, Heterozygous | 0.286166 | Pigmentation allele. | 1 |
| 27 | 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 |
| 28 | 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 |
| 29 | PCSK9-G670E | Low | Uncertain | Uncertain benign Unknown, Homozygous | 0.888269 | This variant is likely benign. | 1 |
| 30 | AMPD1-P48L | Low | Uncertain | Uncertain benign Unknown, Heterozygous | 0.0940695 | Probably benign, ancestral to15173240 pathogenic Q12X mutation. | 1 |
| 31 | APOB-Y1422C | Low | Uncertain | Uncertain benign Unknown, Homozygous | 0.999628 | This position is almost certainly an error in the HG18 reference sequence. | 1 |
| 32 | DSPP-R68W | Low | Uncertain | Uncertain benign Unknown, Heterozygous | 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 |
| 33 | PKP2-L366P | Low | Uncertain | Uncertain benign Unknown, Heterozygous | 0.221231 | This variant is a benign polymorphism. | 1 |
| 34 | 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 |
| 35 | PTCH1-P1315L | Low | Uncertain | Uncertain benign Unknown, Homozygous | 0.29631 | Common polymorphism, presumed benign. | 1 |
| 36 | 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 |
| Row number | Variant | Prioritization score | Allele freq | Num of articles | Zygosity and Prioritization Score Reasons | Sufficient |
|---|