Variant chr15-27871136-T-C details in Genebe, Genetics Data Aggregator

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+18A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0393 in 1,592,268 control chromosomes in the GnomAD database, including 1,436 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.038 ( 124 hom., cov: 33)

Exomes 𝑓: 0.039 ( 1312 hom. )

Consequence

OCA2
NM_000275.3 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: -0.849

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]

OCA2 links:

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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 15-27871136-T-C is Benign according to our data. Variant chr15-27871136-T-C is described in ClinVar as [Benign]. Clinvar id is 195558.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0543 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
OCA2	NM_000275.3 linkuse as main transcript	c.2244+18A>G		intron_variant		ENST00000354638.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
OCA2	ENST00000354638.8 linkuse as main transcript	c.2244+18A>G		intron_variant		1	NM_000275.3	P1	Q04671-1
OCA2	ENST00000353809.9 linkuse as main transcript	c.2172+18A>G		intron_variant		1			Q04671-2

Frequencies

GnomAD3 genomes

AF:

0.0381

AC:

5800

AN:

152122

Hom.:

124

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0436

Gnomad AMI

AF:

0.0219

Gnomad AMR

AF:

0.0295

Gnomad ASJ

AF:

0.0289

Gnomad EAS

AF:

0.000579

Gnomad SAS

AF:

0.0607

Gnomad FIN

AF:

0.0264

Gnomad MID

AF:

0.0475

Gnomad NFE

AF:

0.0401

Gnomad OTH

AF:

0.0489

GnomAD3 exomes

AF:

0.0372

AC:

9345

AN:

251064

Hom.:

225

AF XY:

0.0397

AC XY:

5384

AN XY:

135724

show subpopulations

Gnomad AFR exome

AF:

0.0439

Gnomad AMR exome

AF:

0.0187

Gnomad ASJ exome

AF:

0.0317

Gnomad EAS exome

AF:

0.000163

Gnomad SAS exome

AF:

0.0671

Gnomad FIN exome

AF:

0.0282

Gnomad NFE exome

AF:

0.0418

Gnomad OTH exome

AF:

0.0426

GnomAD4 exome

AF:

0.0395

AC:

56814

AN:

1440028

Hom.:

1312

Cov.:

AF XY:

0.0406

AC XY:

29105

AN XY:

717664

show subpopulations

Gnomad4 AFR exome

AF:

0.0410

Gnomad4 AMR exome

AF:

0.0200

Gnomad4 ASJ exome

AF:

0.0275

Gnomad4 EAS exome

AF:

0.000101

Gnomad4 SAS exome

AF:

0.0677

Gnomad4 FIN exome

AF:

0.0321

Gnomad4 NFE exome

AF:

0.0398

Gnomad4 OTH exome

AF:

0.0408

GnomAD4 genome

AF:

0.0381

AC:

5798

AN:

152240

Hom.:

124

Cov.:

AF XY:

0.0370

AC XY:

2752

AN XY:

74428

show subpopulations

Gnomad4 AFR

AF:

0.0436

Gnomad4 AMR

AF:

0.0295

Gnomad4 ASJ

AF:

0.0289

Gnomad4 EAS

AF:

0.000580

Gnomad4 SAS

AF:

0.0600

Gnomad4 FIN

AF:

0.0264

Gnomad4 NFE

AF:

0.0401

Gnomad4 OTH

AF:

0.0474

Alfa

AF:

0.0418

Hom.:

Bravo

AF:

0.0386

Asia WGS

AF:

0.0270

AC:

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:2

Benign, criteria provided, single submitter	clinical testing	PreventionGenetics, part of Exact Sciences	-	- -
Benign, criteria provided, single submitter	clinical testing	Eurofins Ntd Llc (ga)	Dec 18, 2014	- -

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	Invitae	Jan 31, 2024	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Oct 28, 2020	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.41

DANN

Benign

0.27

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over