rs2202157

Positions:

• chr3-26501929-C-T

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;