rs2202157

Variant names:

• chr3-26501929-C-T
• rs2202157

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 0.127 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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.0321

Gnomad4 AMR AF: 0.134

Gnomad4 ASJ AF: 0.104

Gnomad4 EAS AF: 0.250

Gnomad4 SAS AF: 0.157

Gnomad4 FIN AF: 0.225

Gnomad4 NFE AF: 0.158

Gnomad4 OTH AF: 0.117

Alfa AF: 0.145 Hom.: 414

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2202157; hg19: chr3-26543420;