rs1107267

Variant names:

• chr15-27726493-G-A
• rs1107267
• XM_017022258.2:c.2457-7165C>T

Your query was ambiguous. Multiple possible variants found:

• chr15-27726493-G-A
• chr15-27726493-G-T

Variant summary

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

The XM_017022258.2(OCA2):​c.2457-7165C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.274 in 152,052 control chromosomes in the GnomAD database, including 5,887 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 0.27 (5887 hom., cov: 33)
• Consequence: OCA2 XM_017022258.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.953
• Publications: 4 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: ClinGen, Orphanet, G2P, Labcorp Genetics (formerly Invitae), Ambry Genetics

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.381 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.274 AC: 41608 AN: 151934 Hom.: 5882 Cov.: 33

Gnomad AFR AF: 0.267

Gnomad AMI AF: 0.435

Gnomad AMR AF: 0.293

Gnomad ASJ AF: 0.408

Gnomad EAS AF: 0.365

Gnomad SAS AF: 0.395

Gnomad FIN AF: 0.238

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.253

Gnomad OTH AF: 0.323

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

GnomAD4 genome AF: 0.274 AC: 41619 AN: 152052 Hom.: 5887 Cov.: 33 AF XY: 0.276 AC XY: 20534 AN XY: 74306

African (AFR) AF: 0.266 AC: 11036 AN: 41454

American (AMR) AF: 0.292 AC: 4468 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.408 AC: 1415 AN: 3470

East Asian (EAS) AF: 0.365 AC: 1882 AN: 5158

South Asian (SAS) AF: 0.395 AC: 1907 AN: 4822

European-Finnish (FIN) AF: 0.238 AC: 2516 AN: 10560

Middle Eastern (MID) AF: 0.350 AC: 103 AN: 294

European-Non Finnish (NFE) AF: 0.253 AC: 17206 AN: 67984

Other (OTH) AF: 0.326 AC: 689 AN: 2112

Alfa AF: 0.269 Hom.: 11942

Bravo AF: 0.276

Asia WGS AF: 0.418 AC: 1452 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.68
DANN	Benign	0.40
PhyloP100		-0.95

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1107267; hg19: chr15-27971639;