rs17565841

Positions:

• chr15-27752101-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XM_017022258.2(OCA2):​c.2457-32773C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.102 in 152,236 control chromosomes in the GnomAD database, including 890 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 0.10 (890 hom., cov: 33)
• Consequence: OCA2 XM_017022258.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.99

Genes affected

OCA2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.141 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OCA2	XM_017022258.2	c.2457-32773C>T		intron_variant			XP_016877747.1
OCA2	XM_017022264.2	c.2292-32773C>T		intron_variant			XP_016877753.1
OCA2	XM_047432606.1	c.2433-32773C>T		intron_variant			XP_047288562.1

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.102 AC: 15588 AN: 152118 Hom.: 889 Cov.: 33

Gnomad AFR AF: 0.0646

Gnomad AMI AF: 0.202

Gnomad AMR AF: 0.142

Gnomad ASJ AF: 0.180

Gnomad EAS AF: 0.0840

Gnomad SAS AF: 0.149

Gnomad FIN AF: 0.0858

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.111

Gnomad OTH AF: 0.128

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

GnomAD4 genome AF: 0.102 AC: 15601 AN: 152236 Hom.: 890 Cov.: 33 AF XY: 0.103 AC XY: 7664 AN XY: 74428

Gnomad4 AFR AF: 0.0645

Gnomad4 AMR AF: 0.142

Gnomad4 ASJ AF: 0.180

Gnomad4 EAS AF: 0.0844

Gnomad4 SAS AF: 0.150

Gnomad4 FIN AF: 0.0858

Gnomad4 NFE AF: 0.111

Gnomad4 OTH AF: 0.131

Alfa AF: 0.110 Hom.: 1144

Bravo AF: 0.106

Asia WGS AF: 0.0990 AC: 344 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.11
DANN	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17565841; hg19: chr15-27997247;