rs2638358

Variant names:

• chr3-148688750-C-T
• rs2638358

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 0.201 in 152,006 control chromosomes in the GnomAD database, including 3,399 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 (3399 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.78
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.271 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: 0.201 AC: 30467 AN: 151888 Hom.: 3390 Cov.: 31

Gnomad AFR AF: 0.275

Gnomad AMI AF: 0.258

Gnomad AMR AF: 0.153

Gnomad ASJ AF: 0.287

Gnomad EAS AF: 0.118

Gnomad SAS AF: 0.128

Gnomad FIN AF: 0.141

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.181

Gnomad OTH AF: 0.210

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

GnomAD4 genome AF: 0.201 AC: 30501 AN: 152006 Hom.: 3399 Cov.: 31 AF XY: 0.198 AC XY: 14682 AN XY: 74304

African (AFR) AF: 0.276 AC: 11426 AN: 41444

American (AMR) AF: 0.153 AC: 2332 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.287 AC: 996 AN: 3466

East Asian (EAS) AF: 0.119 AC: 613 AN: 5172

South Asian (SAS) AF: 0.126 AC: 608 AN: 4812

European-Finnish (FIN) AF: 0.141 AC: 1489 AN: 10564

Middle Eastern (MID) AF: 0.269 AC: 79 AN: 294

European-Non Finnish (NFE) AF: 0.181 AC: 12285 AN: 67964

Other (OTH) AF: 0.208 AC: 438 AN: 2110

Alfa AF: 0.186 Hom.: 496

Bravo AF: 0.204

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	-0.99
CADD	Benign	0.076
DANN	Benign	0.71
PhyloP100		-2.8

Splicing

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

Other links and lift over

dbSNP: rs2638358; hg19: chr3-148406537;