2-150776690-G-A

Variant names:

• chr2-150776690-G-A
• rs1519761

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 14 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	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

African (AFR) AF: 0.562 AC: 22990 AN: 40898

American (AMR) AF: 0.664 AC: 10060 AN: 15140

Ashkenazi Jewish (ASJ) AF: 0.528 AC: 1830 AN: 3468

East Asian (EAS) AF: 0.593 AC: 3032 AN: 5110

South Asian (SAS) AF: 0.588 AC: 2810 AN: 4780

European-Finnish (FIN) AF: 0.444 AC: 4489 AN: 10112

Middle Eastern (MID) AF: 0.559 AC: 162 AN: 290

European-Non Finnish (NFE) AF: 0.596 AC: 40410 AN: 67852

Other (OTH) AF: 0.575 AC: 1201 AN: 2088

Alfa AF: 0.586 Hom.: 31154

Bravo AF: 0.598

Asia WGS AF: 0.599 AC: 2086 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.0
DANN	Benign	0.13
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs1519761; hg19: chr2-151633204;