15-27871190-C-A
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_StrongBP6BP7BS2_Supporting
The NM_000275.3(OCA2):c.2208G>T(p.Ser736=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000564 in 1,614,020 control chromosomes in the GnomAD database, including 6 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. S736S) has been classified as Benign.
Frequency
Consequence
NM_000275.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
OCA2 | NM_000275.3 | c.2208G>T | p.Ser736= | synonymous_variant | 21/24 | ENST00000354638.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OCA2 | ENST00000354638.8 | c.2208G>T | p.Ser736= | synonymous_variant | 21/24 | 1 | NM_000275.3 | P1 | |
OCA2 | ENST00000353809.9 | c.2136G>T | p.Ser712= | synonymous_variant | 20/23 | 1 |
Frequencies
GnomAD3 genomes AF: 0.00322 AC: 489AN: 152052Hom.: 2 Cov.: 33
GnomAD3 exomes AF: 0.000827 AC: 208AN: 251366Hom.: 1 AF XY: 0.000655 AC XY: 89AN XY: 135864
GnomAD4 exome AF: 0.000289 AC: 422AN: 1461850Hom.: 4 Cov.: 32 AF XY: 0.000257 AC XY: 187AN XY: 727232
GnomAD4 genome AF: 0.00321 AC: 489AN: 152170Hom.: 2 Cov.: 33 AF XY: 0.00289 AC XY: 215AN XY: 74384
ClinVar
Submissions by phenotype
Tyrosinase-positive oculocutaneous albinism Uncertain:1Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Nov 07, 2021 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 13, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease. - |
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Feb 29, 2016 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at