rs7586540

Variant names:

• chr2-5912619-G-A
• rs7586540

Your query was ambiguous. Multiple possible variants found:

• chr2-5912619-G-A
• chr2-5912619-G-C
• chr2-5912619-G-T

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 0.893 in 152,120 control chromosomes in the GnomAD database, including 60,849 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 0.89 (60849 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0310
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 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: 0.893 AC: 135694 AN: 152002 Hom.: 60787 Cov.: 30

Gnomad AFR AF: 0.943

Gnomad AMI AF: 0.823

Gnomad AMR AF: 0.898

Gnomad ASJ AF: 0.840

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.947

Gnomad FIN AF: 0.899

Gnomad MID AF: 0.820

Gnomad NFE AF: 0.852

Gnomad OTH AF: 0.870

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

GnomAD4 genome AF: 0.893 AC: 135816 AN: 152120 Hom.: 60849 Cov.: 30 AF XY: 0.897 AC XY: 66679 AN XY: 74348

African (AFR) AF: 0.943 AC: 39177 AN: 41524

American (AMR) AF: 0.899 AC: 13727 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.840 AC: 2912 AN: 3468

East Asian (EAS) AF: 0.999 AC: 5145 AN: 5148

South Asian (SAS) AF: 0.946 AC: 4546 AN: 4804

European-Finnish (FIN) AF: 0.899 AC: 9516 AN: 10588

Middle Eastern (MID) AF: 0.823 AC: 242 AN: 294

European-Non Finnish (NFE) AF: 0.852 AC: 57956 AN: 67992

Other (OTH) AF: 0.872 AC: 1844 AN: 2114

Alfa AF: 0.877 Hom.: 70984

Bravo AF: 0.894

Asia WGS AF: 0.975 AC: 3389 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.6
DANN	Benign	0.43
PhyloP100		0.031

Splicing

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

Other links and lift over

dbSNP: rs7586540; hg19: chr2-6052751;