rs2594902

Positions:

• chr15-27902593-A-G

Variant summary

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

The NM_000275.3(OCA2):​c.2079+23534T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.146 in 152,152 control chromosomes in the GnomAD database, including 4,045 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 0.15 (4045 hom., cov: 33)
• Consequence: OCA2 NM_000275.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.45

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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.419 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OCA2	NM_000275.3	c.2079+23534T>C		intron_variant		ENST00000354638.8	NP_000266.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OCA2	ENST00000354638.8	c.2079+23534T>C		intron_variant		1	NM_000275.3	ENSP00000346659	P1
OCA2	ENST00000353809.9	c.2007+23534T>C		intron_variant		1		ENSP00000261276

Frequencies

GnomAD3 genomes AF: 0.146 AC: 22235 AN: 152034 Hom.: 4038 Cov.: 33

Gnomad AFR AF: 0.424

Gnomad AMI AF: 0.0164

Gnomad AMR AF: 0.0571

Gnomad ASJ AF: 0.00922

Gnomad EAS AF: 0.0332

Gnomad SAS AF: 0.279

Gnomad FIN AF: 0.0121

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0280

Gnomad OTH AF: 0.106

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

GnomAD4 genome AF: 0.146 AC: 22290 AN: 152152 Hom.: 4045 Cov.: 33 AF XY: 0.146 AC XY: 10852 AN XY: 74396

Gnomad4 AFR AF: 0.424

Gnomad4 AMR AF: 0.0570

Gnomad4 ASJ AF: 0.00922

Gnomad4 EAS AF: 0.0333

Gnomad4 SAS AF: 0.279

Gnomad4 FIN AF: 0.0121

Gnomad4 NFE AF: 0.0280

Gnomad4 OTH AF: 0.107

Alfa AF: 0.0923 Hom.: 288

Bravo AF: 0.155

Asia WGS AF: 0.203 AC: 704 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.87
DANN	Benign	0.59

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: rs2594902; hg19: chr15-28147739;