rs1448484

chr15-28038295-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.228-6132T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.203 in 152,162 control chromosomes in the GnomAD database, including 10,238 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 0.20 (10238 hom., cov: 32)
• Consequence: OCA2 NM_000275.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0460

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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.688 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
OCA2	NM_000275.3	c.228-6132T>C		intron_variant		ENST00000354638.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
OCA2	ENST00000354638.8	c.228-6132T>C		intron_variant		1	NM_000275.3	P1
OCA2	ENST00000353809.9	c.228-6132T>C		intron_variant		1
OCA2	ENST00000431101.1	c.228-6132T>C		intron_variant		3
OCA2	ENST00000445578.5	c.228-6132T>C		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.202 AC: 30724 AN: 152044 Hom.: 10190 Cov.: 32

Gnomad AFR AF: 0.695

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0737

Gnomad ASJ AF: 0.0199

Gnomad EAS AF: 0.000386

Gnomad SAS AF: 0.0416

Gnomad FIN AF: 0.000188

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.00423

Gnomad OTH AF: 0.148

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

GnomAD4 genome AF: 0.203 AC: 30839 AN: 152162 Hom.: 10238 Cov.: 32 AF XY: 0.195 AC XY: 14533 AN XY: 74426

Gnomad4 AFR AF: 0.695

Gnomad4 AMR AF: 0.0736

Gnomad4 ASJ AF: 0.0199

Gnomad4 EAS AF: 0.000387

Gnomad4 SAS AF: 0.0412

Gnomad4 FIN AF: 0.000188

Gnomad4 NFE AF: 0.00423

Gnomad4 OTH AF: 0.153

Alfa AF: 0.0446 Hom.: 2800

Asia WGS AF: 0.0950 AC: 331 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	1.7
Dann	Benign	0.65

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: rs1448484; hg19: chr15-28283441;