15-27871129-G-C
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_000275.3(OCA2):c.2244+25C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.724 in 1,569,672 control chromosomes in the GnomAD database, including 419,793 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.79 ( 48096 hom., cov: 32)
Exomes 𝑓: 0.72 ( 371697 hom. )
Consequence
OCA2
NM_000275.3 intron
NM_000275.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.358
Genes affected
OCA2 (HGNC:8101): (OCA2 melanosomal transmembrane protein) This gene encodes the human homolog of the mouse p (pink-eyed dilution) gene. The encoded protein is believed to be an integral membrane protein involved in small molecule transport, specifically tyrosine, which is a precursor to melanin synthesis. It is involved in mammalian pigmentation, where it may control skin color variation and act as a determinant of brown or blue eye color. Mutations in this gene result in type 2 oculocutaneous albinism. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2014]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BP6
?
Variant 15-27871129-G-C is Benign according to our data. Variant chr15-27871129-G-C is described in ClinVar as [Benign]. Clinvar id is 1263011.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
OCA2 | NM_000275.3 | c.2244+25C>G | intron_variant | ENST00000354638.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OCA2 | ENST00000354638.8 | c.2244+25C>G | intron_variant | 1 | NM_000275.3 | P1 | |||
OCA2 | ENST00000353809.9 | c.2172+25C>G | intron_variant | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.786 AC: 119468AN: 152028Hom.: 48033 Cov.: 32
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GnomAD3 exomes AF: 0.781 AC: 195456AN: 250336Hom.: 78174 AF XY: 0.780 AC XY: 105582AN XY: 135310
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GnomAD4 exome AF: 0.718 AC: 1017568AN: 1417526Hom.: 371697 Cov.: 24 AF XY: 0.723 AC XY: 511321AN XY: 707690
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GnomAD4 genome ? AF: 0.786 AC: 119591AN: 152146Hom.: 48096 Cov.: 32 AF XY: 0.790 AC XY: 58754AN XY: 74372
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Tyrosinase-positive oculocutaneous albinism Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Sep 05, 2021 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 12, 2018 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at