rs7586694

chr2-82431224-G-A

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 0.394 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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

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

Gnomad4 AFR AF: 0.664

Gnomad4 AMR AF: 0.285

Gnomad4 ASJ AF: 0.327

Gnomad4 EAS AF: 0.0308

Gnomad4 SAS AF: 0.202

Gnomad4 FIN AF: 0.273

Gnomad4 NFE AF: 0.319

Gnomad4 OTH AF: 0.352

Alfa AF: 0.333 Hom.: 3087

Bravo AF: 0.403

Asia WGS AF: 0.146 AC: 510 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	2.5
Dann	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7586694; hg19: chr2-82658348;