15-27940869-C-T

Variant names:

• chr15-27940869-C-T
• rs1562592
• NM_000275.3:c.1951+10915G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_000275.3(OCA2):​c.1951+10915G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.206 in 152,128 control chromosomes in the GnomAD database, including 3,703 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 0.21 (3703 hom., cov: 33)
• Consequence: OCA2 NM_000275.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.663
• Publications: 2 publications found

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 Gene-Disease associations (from GenCC):

• oculocutaneous albinism type 2

  Inheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), Orphanet, Ambry Genetics, G2P, ClinGen

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.356 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OCA2	NM_000275.3	c.1951+10915G>A		intron_variant	Intron 18 of 23	ENST00000354638.8	NP_000266.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OCA2	ENST00000354638.8	c.1951+10915G>A		intron_variant	Intron 18 of 23	1	NM_000275.3	ENSP00000346659.3
OCA2	ENST00000353809.9	c.1879+10915G>A		intron_variant	Intron 17 of 22	1		ENSP00000261276.8

Frequencies

GnomAD3 genomes AF: 0.205 AC: 31216 AN: 152010 Hom.: 3692 Cov.: 33

Gnomad AFR AF: 0.283

Gnomad AMI AF: 0.0844

Gnomad AMR AF: 0.269

Gnomad ASJ AF: 0.139

Gnomad EAS AF: 0.0112

Gnomad SAS AF: 0.370

Gnomad FIN AF: 0.168

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.158

Gnomad OTH AF: 0.197

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

GnomAD4 genome AF: 0.206 AC: 31265 AN: 152128 Hom.: 3703 Cov.: 33 AF XY: 0.211 AC XY: 15673 AN XY: 74374

African (AFR) AF: 0.284 AC: 11760 AN: 41468

American (AMR) AF: 0.269 AC: 4108 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.139 AC: 481 AN: 3468

East Asian (EAS) AF: 0.0112 AC: 58 AN: 5178

South Asian (SAS) AF: 0.370 AC: 1783 AN: 4818

European-Finnish (FIN) AF: 0.168 AC: 1783 AN: 10586

Middle Eastern (MID) AF: 0.201 AC: 59 AN: 294

European-Non Finnish (NFE) AF: 0.158 AC: 10745 AN: 68022

Other (OTH) AF: 0.195 AC: 411 AN: 2112

Alfa AF: 0.179 Hom.: 532

Bravo AF: 0.206

Asia WGS AF: 0.199 AC: 691 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.86
DANN	Benign	0.61
PhyloP100		-0.66
Mutation Taster		=96/4	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1562592; hg19: chr15-28186015;