rs1375166

Variant summary

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

The NM_000275.3(OCA2):​c.2080-16306G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.19 in 152,158 control chromosomes in the GnomAD database, including 3,926 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 0.19 ( 3926 hom., cov: 32)

Consequence

OCA2
NM_000275.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.210
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=-0.9).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.547 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
OCA2NM_000275.3 linkuse as main transcriptc.2080-16306G>A intron_variant ENST00000354638.8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
OCA2ENST00000354638.8 linkuse as main transcriptc.2080-16306G>A intron_variant 1 NM_000275.3 P1Q04671-1
OCA2ENST00000353809.9 linkuse as main transcriptc.2008-16306G>A intron_variant 1 Q04671-2

Frequencies

GnomAD3 genomes
AF:
0.190
AC:
28834
AN:
152040
Hom.:
3923
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0421
Gnomad AMI
AF:
0.420
Gnomad AMR
AF:
0.326
Gnomad ASJ
AF:
0.320
Gnomad EAS
AF:
0.564
Gnomad SAS
AF:
0.291
Gnomad FIN
AF:
0.255
Gnomad MID
AF:
0.237
Gnomad NFE
AF:
0.193
Gnomad OTH
AF:
0.198
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.190
AC:
28840
AN:
152158
Hom.:
3926
Cov.:
32
AF XY:
0.200
AC XY:
14842
AN XY:
74376
show subpopulations
Gnomad4 AFR
AF:
0.0420
Gnomad4 AMR
AF:
0.327
Gnomad4 ASJ
AF:
0.320
Gnomad4 EAS
AF:
0.564
Gnomad4 SAS
AF:
0.290
Gnomad4 FIN
AF:
0.255
Gnomad4 NFE
AF:
0.193
Gnomad4 OTH
AF:
0.199
Alfa
AF:
0.181
Hom.:
739
Bravo
AF:
0.192
Asia WGS
AF:
0.401
AC:
1394
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
5.2
DANN
Benign
0.38

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: rs1375166; hg19: chr15-28133374; API