Variant rs1900758 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.1364+113G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.607 in 1,282,724 control chromosomes in the GnomAD database, including 261,509 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.49 ( 22736 hom., cov: 33)

Exomes 𝑓: 0.62 ( 238773 hom. )

Consequence

OCA2
NM_000275.3 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.0900

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=-0.83).

BP6

Variant 15-27984951-C-T is Benign according to our data. Variant chr15-27984951-C-T is described in ClinVar as [Benign]. Clinvar id is 1233186.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.698 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OCA2	NM_000275.3 linkuse as main transcript	c.1364+113G>A		intron_variant		ENST00000354638.8	NP_000266.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OCA2	ENST00000354638.8 linkuse as main transcript	c.1364+113G>A		intron_variant		1	NM_000275.3	ENSP00000346659	P1	Q04671-1
OCA2	ENST00000353809.9 linkuse as main transcript	c.1292+113G>A		intron_variant		1		ENSP00000261276		Q04671-2

Frequencies

GnomAD3 genomes

AF:

0.487

AC:

73997

AN:

152008

Hom.:

22742

Cov.:

show subpopulations

Gnomad AFR

AF:

0.181

Gnomad AMI

AF:

0.738

Gnomad AMR

AF:

0.380

Gnomad ASJ

AF:

0.579

Gnomad EAS

AF:

0.0348

Gnomad SAS

AF:

0.284

Gnomad FIN

AF:

0.700

Gnomad MID

AF:

0.620

Gnomad NFE

AF:

0.704

Gnomad OTH

AF:

0.492

GnomAD4 exome

AF:

0.624

AC:

705134

AN:

1130598

Hom.:

238773

AF XY:

0.615

AC XY:

352097

AN XY:

572276

show subpopulations

Gnomad4 AFR exome

AF:

0.171

Gnomad4 AMR exome

AF:

0.302

Gnomad4 ASJ exome

AF:

0.576

Gnomad4 EAS exome

AF:

0.0209

Gnomad4 SAS exome

AF:

0.314

Gnomad4 FIN exome

AF:

0.708

Gnomad4 NFE exome

AF:

0.705

Gnomad4 OTH exome

AF:

0.572

GnomAD4 genome

AF:

0.486

AC:

73975

AN:

152126

Hom.:

22736

Cov.:

AF XY:

0.479

AC XY:

35590

AN XY:

74368

show subpopulations

Gnomad4 AFR

AF:

0.180

Gnomad4 AMR

AF:

0.380

Gnomad4 ASJ

AF:

0.579

Gnomad4 EAS

AF:

0.0348

Gnomad4 SAS

AF:

0.285

Gnomad4 FIN

AF:

0.700

Gnomad4 NFE

AF:

0.704

Gnomad4 OTH

AF:

0.487

Alfa

AF:

0.613

Hom.:

5409

Bravo

AF:

0.452

Asia WGS

AF:

0.184

AC:

645

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 19, 2021	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

1.4

DANN

Benign

0.63

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