rs2157051

Variant names:

• chr6-32690847-G-A
• rs2157051

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 0.695 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
• Publications: 24 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.657 AC: 23133 AN: 35216

American (AMR) AF: 0.714 AC: 9692 AN: 13576

Ashkenazi Jewish (ASJ) AF: 0.749 AC: 2380 AN: 3178

East Asian (EAS) AF: 0.698 AC: 2985 AN: 4278

South Asian (SAS) AF: 0.695 AC: 2761 AN: 3970

European-Finnish (FIN) AF: 0.678 AC: 5786 AN: 8532

Middle Eastern (MID) AF: 0.775 AC: 214 AN: 276

European-Non Finnish (NFE) AF: 0.708 AC: 44316 AN: 62590

Other (OTH) AF: 0.727 AC: 1351 AN: 1858

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
PhyloP100		-0.55

Splicing

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

Other links and lift over

dbSNP: rs2157051; hg19: chr6-32658624;