rs7586694

Variant names:

• chr2-82431224-G-A
• rs7586694

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 0.394 in 148,704 control chromosomes in the GnomAD database, including 13,880 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 0.39 (13880 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0600
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.658 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.394 AC: 58505 AN: 148602 Hom.: 13841 Cov.: 29

Gnomad AFR AF: 0.664

Gnomad AMI AF: 0.313

Gnomad AMR AF: 0.286

Gnomad ASJ AF: 0.327

Gnomad EAS AF: 0.0309

Gnomad SAS AF: 0.202

Gnomad FIN AF: 0.273

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.319

Gnomad OTH AF: 0.356

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

GnomAD4 genome AF: 0.394 AC: 58594 AN: 148704 Hom.: 13880 Cov.: 29 AF XY: 0.387 AC XY: 28027 AN XY: 72482

African (AFR) AF: 0.664 AC: 26878 AN: 40452

American (AMR) AF: 0.285 AC: 4252 AN: 14898

Ashkenazi Jewish (ASJ) AF: 0.327 AC: 1119 AN: 3424

East Asian (EAS) AF: 0.0308 AC: 153 AN: 4974

South Asian (SAS) AF: 0.202 AC: 948 AN: 4682

European-Finnish (FIN) AF: 0.273 AC: 2715 AN: 9958

Middle Eastern (MID) AF: 0.377 AC: 107 AN: 284

European-Non Finnish (NFE) AF: 0.319 AC: 21414 AN: 67070

Other (OTH) AF: 0.352 AC: 727 AN: 2064

Alfa AF: 0.337 Hom.: 3566

Bravo AF: 0.403

Asia WGS AF: 0.146 AC: 510 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.5
DANN	Benign	0.55
PhyloP100		0.060

Splicing

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

Other links and lift over

dbSNP: rs7586694; hg19: chr2-82658348;