15-27994155-A-G

Variant names:

• chr15-27994155-A-G
• rs2015343
• NM_000275.3:c.1045-3508T>C

Variant summary

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

The NM_000275.3(OCA2):​c.1045-3508T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.603 in 151,994 control chromosomes in the GnomAD database, including 31,789 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 0.60 (31789 hom., cov: 32)
• Consequence: OCA2 NM_000275.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.502
• Publications: 3 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=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.789 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000275.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OCA2	NM_000275.3	MANE Select	c.1045-3508T>C		intron	N/A	NP_000266.2
	OCA2	NM_001300984.2		c.1045-4489T>C		intron	N/A	NP_001287913.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OCA2	ENST00000354638.8	TSL:1 MANE Select	c.1045-3508T>C		intron	N/A	ENSP00000346659.3
	OCA2	ENST00000353809.9	TSL:1	c.1045-4489T>C		intron	N/A	ENSP00000261276.8
	OCA2	ENST00000910120.1		c.1045-3508T>C		intron	N/A	ENSP00000580179.1

Frequencies

GnomAD3 genomes AF: 0.603 AC: 91582 AN: 151876 Hom.: 31794 Cov.: 32

Gnomad AFR AF: 0.274

Gnomad AMI AF: 0.771

Gnomad AMR AF: 0.573

Gnomad ASJ AF: 0.716

Gnomad EAS AF: 0.397

Gnomad SAS AF: 0.371

Gnomad FIN AF: 0.839

Gnomad MID AF: 0.759

Gnomad NFE AF: 0.795

Gnomad OTH AF: 0.639

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

GnomAD4 genome AF: 0.603 AC: 91581 AN: 151994 Hom.: 31789 Cov.: 32 AF XY: 0.600 AC XY: 44567 AN XY: 74296

African (AFR) AF: 0.274 AC: 11361 AN: 41450

American (AMR) AF: 0.573 AC: 8741 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.716 AC: 2480 AN: 3466

East Asian (EAS) AF: 0.397 AC: 2041 AN: 5142

South Asian (SAS) AF: 0.370 AC: 1776 AN: 4794

European-Finnish (FIN) AF: 0.839 AC: 8881 AN: 10586

Middle Eastern (MID) AF: 0.769 AC: 226 AN: 294

European-Non Finnish (NFE) AF: 0.795 AC: 54034 AN: 67972

Other (OTH) AF: 0.633 AC: 1339 AN: 2114

Alfa AF: 0.673 Hom.: 4940

Bravo AF: 0.576

Asia WGS AF: 0.457 AC: 1590 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	3.5
DANN	Benign	0.67
PhyloP100		-0.50
Mutation Taster		=100/0	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: rs2015343; hg19: chr15-28239301;