15-27761160-C-T

Position:

• chr15-27761160-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000354638.8(OCA2):​c.2433-5688G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.638 in 151,476 control chromosomes in the GnomAD database, including 31,074 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 0.64 (31074 hom., cov: 29)
• Consequence: OCA2 ENST00000354638.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.27

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.696 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OCA2	NM_000275.3	c.2433-5688G>A		intron_variant		ENST00000354638.8	NP_000266.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OCA2	ENST00000354638.8	c.2433-5688G>A		intron_variant		1	NM_000275.3	ENSP00000346659	P1
OCA2	ENST00000353809.9	c.2361-5688G>A		intron_variant		1		ENSP00000261276

Frequencies

GnomAD3 genomes AF: 0.638 AC: 96543 AN: 151358 Hom.: 31040 Cov.: 29

Gnomad AFR AF: 0.686

Gnomad AMI AF: 0.405

Gnomad AMR AF: 0.607

Gnomad ASJ AF: 0.542

Gnomad EAS AF: 0.715

Gnomad SAS AF: 0.654

Gnomad FIN AF: 0.679

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.613

Gnomad OTH AF: 0.574

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.638 AC: 96631 AN: 151476 Hom.: 31074 Cov.: 29 AF XY: 0.639 AC XY: 47305 AN XY: 74004

Gnomad4 AFR AF: 0.686

Gnomad4 AMR AF: 0.607

Gnomad4 ASJ AF: 0.542

Gnomad4 EAS AF: 0.715

Gnomad4 SAS AF: 0.654

Gnomad4 FIN AF: 0.679

Gnomad4 NFE AF: 0.613

Gnomad4 OTH AF: 0.577

Alfa AF: 0.621 Hom.: 14227

Bravo AF: 0.634

Asia WGS AF: 0.711 AC: 2462 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.24
DANN	Benign	0.081

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

Other links and lift over

dbSNP: rs989869; hg19: chr15-28006306;