rs2202157

Variant names:

• chr3-26501929-C-T
• rs2202157

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 0.127 in 152,024 control chromosomes in the GnomAD database, including 1,602 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 0.13 (1602 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.410
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.239 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: 0.127 AC: 19337 AN: 151906 Hom.: 1604 Cov.: 32

Gnomad AFR AF: 0.0322

Gnomad AMI AF: 0.226

Gnomad AMR AF: 0.134

Gnomad ASJ AF: 0.104

Gnomad EAS AF: 0.250

Gnomad SAS AF: 0.157

Gnomad FIN AF: 0.225

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.158

Gnomad OTH AF: 0.117

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

GnomAD4 genome AF: 0.127 AC: 19333 AN: 152024 Hom.: 1602 Cov.: 32 AF XY: 0.131 AC XY: 9754 AN XY: 74286

African (AFR) AF: 0.0321 AC: 1334 AN: 41510

American (AMR) AF: 0.134 AC: 2038 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.104 AC: 361 AN: 3470

East Asian (EAS) AF: 0.250 AC: 1291 AN: 5162

South Asian (SAS) AF: 0.157 AC: 757 AN: 4826

European-Finnish (FIN) AF: 0.225 AC: 2372 AN: 10524

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.158 AC: 10708 AN: 67962

Other (OTH) AF: 0.117 AC: 246 AN: 2110

Alfa AF: 0.144 Hom.: 636

Bravo AF: 0.116

Asia WGS AF: 0.171 AC: 598 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.36
DANN	Benign	0.16
PhyloP100		-0.41

Splicing

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

Other links and lift over

dbSNP: rs2202157; hg19: chr3-26543420;