rs2638359

Variant names:

• chr3-148688596-A-T
• rs2638359

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 0.18 in 152,080 control chromosomes in the GnomAD database, including 2,622 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 0.18 (2622 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.975
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.199 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: 0.180 AC: 27317 AN: 151964 Hom.: 2616 Cov.: 32

Gnomad AFR AF: 0.203

Gnomad AMI AF: 0.258

Gnomad AMR AF: 0.146

Gnomad ASJ AF: 0.287

Gnomad EAS AF: 0.117

Gnomad SAS AF: 0.128

Gnomad FIN AF: 0.141

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.181

Gnomad OTH AF: 0.195

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

GnomAD4 genome AF: 0.180 AC: 27345 AN: 152080 Hom.: 2622 Cov.: 32 AF XY: 0.178 AC XY: 13221 AN XY: 74340

African (AFR) AF: 0.203 AC: 8411 AN: 41460

American (AMR) AF: 0.146 AC: 2231 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.287 AC: 996 AN: 3468

East Asian (EAS) AF: 0.118 AC: 608 AN: 5164

South Asian (SAS) AF: 0.126 AC: 608 AN: 4808

European-Finnish (FIN) AF: 0.141 AC: 1492 AN: 10602

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.181 AC: 12278 AN: 67988

Other (OTH) AF: 0.193 AC: 408 AN: 2114

Alfa AF: 0.179 Hom.: 312

Bravo AF: 0.181

Asia WGS AF: 0.127 AC: 447 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	8.2
DANN	Benign	0.87
PhyloP100		0.97

Splicing

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

Other links and lift over

dbSNP: rs2638359; hg19: chr3-148406383;