rs2638357

Positions:

• chr3-148688832-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 0.195 in 152,002 control chromosomes in the GnomAD database, including 3,166 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 0.20 (3166 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0290

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.252 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: 0.195 AC: 29631 AN: 151884 Hom.: 3157 Cov.: 32

Gnomad AFR AF: 0.256

Gnomad AMI AF: 0.258

Gnomad AMR AF: 0.152

Gnomad ASJ AF: 0.287

Gnomad EAS AF: 0.119

Gnomad SAS AF: 0.127

Gnomad FIN AF: 0.141

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.181

Gnomad OTH AF: 0.207

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

GnomAD4 genome AF: 0.195 AC: 29666 AN: 152002 Hom.: 3166 Cov.: 32 AF XY: 0.192 AC XY: 14280 AN XY: 74302

Gnomad4 AFR AF: 0.256

Gnomad4 AMR AF: 0.152

Gnomad4 ASJ AF: 0.287

Gnomad4 EAS AF: 0.119

Gnomad4 SAS AF: 0.126

Gnomad4 FIN AF: 0.141

Gnomad4 NFE AF: 0.181

Gnomad4 OTH AF: 0.205

Alfa AF: 0.188 Hom.: 635

Bravo AF: 0.198

Asia WGS AF: 0.131 AC: 462 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.6
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2638357; hg19: chr3-148406619;