rs977588

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_000275.3(OCA2):​c.1952-7906G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.533 in 150,246 control chromosomes in the GnomAD database, including 22,068 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.53 ( 22068 hom., cov: 31)

Consequence

OCA2
NM_000275.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.213
Variant links:
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 -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-1.01).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.593 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
OCA2NM_000275.3 linkuse as main transcriptc.1952-7906G>T intron_variant ENST00000354638.8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
OCA2ENST00000354638.8 linkuse as main transcriptc.1952-7906G>T intron_variant 1 NM_000275.3 P1Q04671-1
OCA2ENST00000353809.9 linkuse as main transcriptc.1880-7906G>T intron_variant 1 Q04671-2

Frequencies

GnomAD3 genomes
AF:
0.533
AC:
80016
AN:
150138
Hom.:
22062
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.530
Gnomad AMI
AF:
0.675
Gnomad AMR
AF:
0.450
Gnomad ASJ
AF:
0.516
Gnomad EAS
AF:
0.193
Gnomad SAS
AF:
0.215
Gnomad FIN
AF:
0.555
Gnomad MID
AF:
0.523
Gnomad NFE
AF:
0.597
Gnomad OTH
AF:
0.518
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.533
AC:
80057
AN:
150246
Hom.:
22068
Cov.:
31
AF XY:
0.521
AC XY:
38201
AN XY:
73288
show subpopulations
Gnomad4 AFR
AF:
0.530
Gnomad4 AMR
AF:
0.449
Gnomad4 ASJ
AF:
0.516
Gnomad4 EAS
AF:
0.193
Gnomad4 SAS
AF:
0.216
Gnomad4 FIN
AF:
0.555
Gnomad4 NFE
AF:
0.597
Gnomad4 OTH
AF:
0.522
Alfa
AF:
0.562
Hom.:
30666
Bravo
AF:
0.525
Asia WGS
AF:
0.247
AC:
863
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
0.72
DANN
Benign
0.42

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs977588; hg19: chr15-28179306; API