rs1519761

Variant names:

• chr2-150776690-G-A
• rs1519761

Your query was ambiguous. Multiple possible variants found:

• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;