rs1519761

Positions:

• chr2-150776690-G-A
• chr2-150776690-G-C

Variant summary

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

The variant allele was found at a frequency of 0.582 in 150,648 control chromosomes in the GnomAD database, including 25,776 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 0.58 (25776 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.133

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.654 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.582 AC: 87583 AN: 150550 Hom.: 25760 Cov.: 29

Gnomad AFR AF: 0.563

Gnomad AMI AF: 0.710

Gnomad AMR AF: 0.664

Gnomad ASJ AF: 0.528

Gnomad EAS AF: 0.594

Gnomad SAS AF: 0.587

Gnomad FIN AF: 0.444

Gnomad MID AF: 0.558

Gnomad NFE AF: 0.596

Gnomad OTH AF: 0.574

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

GnomAD4 genome AF: 0.582 AC: 87630 AN: 150648 Hom.: 25776 Cov.: 29 AF XY: 0.576 AC XY: 42314 AN XY: 73452

Gnomad4 AFR AF: 0.562

Gnomad4 AMR AF: 0.664

Gnomad4 ASJ AF: 0.528

Gnomad4 EAS AF: 0.593

Gnomad4 SAS AF: 0.588

Gnomad4 FIN AF: 0.444

Gnomad4 NFE AF: 0.596

Gnomad4 OTH AF: 0.575

Alfa AF: 0.585 Hom.: 25594

Bravo AF: 0.598

Asia WGS AF: 0.599 AC: 2086 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.0
DANN	Benign	0.13

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1519761; hg19: chr2-151633204;