rs2157051

chr6-32690847-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 0.695 in 134,354 control chromosomes in the GnomAD database, including 29,423 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 0.69 (29423 hom., cov: 26)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.548

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.703 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: 0.695 AC: 93270 AN: 134256 Hom.: 29403 Cov.: 26

Gnomad AFR AF: 0.657

Gnomad AMI AF: 0.818

Gnomad AMR AF: 0.714

Gnomad ASJ AF: 0.749

Gnomad EAS AF: 0.698

Gnomad SAS AF: 0.696

Gnomad FIN AF: 0.678

Gnomad MID AF: 0.776

Gnomad NFE AF: 0.708

Gnomad OTH AF: 0.726

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

GnomAD4 genome AF: 0.695 AC: 93338 AN: 134354 Hom.: 29423 Cov.: 26 AF XY: 0.693 AC XY: 45211 AN XY: 65228

Gnomad4 AFR AF: 0.657

Gnomad4 AMR AF: 0.714

Gnomad4 ASJ AF: 0.749

Gnomad4 EAS AF: 0.698

Gnomad4 SAS AF: 0.695

Gnomad4 FIN AF: 0.678

Gnomad4 NFE AF: 0.708

Gnomad4 OTH AF: 0.727

Alfa AF: 0.647 Hom.: 3057

Bravo AF: 0.627

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	2.4
Dann	Benign	0.21

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2157051; hg19: chr6-32658624;