rs1107267

Positions:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

OCA2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OCA2	XM_017022258.2	c.2457-7165C>T		intron_variant			XP_016877747.1
OCA2	XM_017022264.2	c.2292-7165C>T		intron_variant			XP_016877753.1
OCA2	XM_047432606.1	c.2433-7165C>T		intron_variant			XP_047288562.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.266

Gnomad4 AMR AF: 0.292

Gnomad4 ASJ AF: 0.408

Gnomad4 EAS AF: 0.365

Gnomad4 SAS AF: 0.395

Gnomad4 FIN AF: 0.238

Gnomad4 NFE AF: 0.253

Gnomad4 OTH AF: 0.326

Alfa AF: 0.267 Hom.: 7528

Bravo AF: 0.276

Asia WGS AF: 0.418 AC: 1452 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1107267; hg19: chr15-27971639;