rs767182132
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4_StrongBP7
The NM_000275.3(OCA2):c.1047C>T(p.Ile349=) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000564 in 1,613,608 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_000275.3 splice_region, synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
OCA2 | NM_000275.3 | c.1047C>T | p.Ile349= | splice_region_variant, synonymous_variant | 10/24 | ENST00000354638.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OCA2 | ENST00000354638.8 | c.1047C>T | p.Ile349= | splice_region_variant, synonymous_variant | 10/24 | 1 | NM_000275.3 | P1 | |
OCA2 | ENST00000353809.9 | c.1045-979C>T | intron_variant | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000920 AC: 14AN: 152166Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000877 AC: 22AN: 250948Hom.: 0 AF XY: 0.0000737 AC XY: 10AN XY: 135640
GnomAD4 exome AF: 0.0000527 AC: 77AN: 1461442Hom.: 0 Cov.: 34 AF XY: 0.0000550 AC XY: 40AN XY: 727034
GnomAD4 genome ? AF: 0.0000920 AC: 14AN: 152166Hom.: 0 Cov.: 33 AF XY: 0.000108 AC XY: 8AN XY: 74348
ClinVar
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Mar 01, 2023 | OCA2: BP4, BP7 - |
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 25, 2024 | - - |
Tyrosinase-positive oculocutaneous albinism Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | Laboratoire de Génétique Moléculaire, CHU Bordeaux | - | - - |
OCA2-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | May 29, 2020 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at