3-137389640-T-C

Variant names:

• chr3-137389640-T-C
• rs1382269

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 0.393 in 152,146 control chromosomes in the GnomAD database, including 13,011 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 0.39 (13011 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.985
• Publications: 12 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 (AMR) allele frequency at 95% confidence interval = 0.519 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: 0.393 AC: 59715 AN: 152028 Hom.: 13001 Cov.: 32

Gnomad AFR AF: 0.216

Gnomad AMI AF: 0.596

Gnomad AMR AF: 0.528

Gnomad ASJ AF: 0.479

Gnomad EAS AF: 0.353

Gnomad SAS AF: 0.246

Gnomad FIN AF: 0.385

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.476

Gnomad OTH AF: 0.437

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

GnomAD4 genome AF: 0.393 AC: 59744 AN: 152146 Hom.: 13011 Cov.: 32 AF XY: 0.390 AC XY: 29045 AN XY: 74380

African (AFR) AF: 0.216 AC: 8946 AN: 41512

American (AMR) AF: 0.529 AC: 8083 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.479 AC: 1662 AN: 3470

East Asian (EAS) AF: 0.353 AC: 1821 AN: 5164

South Asian (SAS) AF: 0.246 AC: 1185 AN: 4826

European-Finnish (FIN) AF: 0.385 AC: 4073 AN: 10582

Middle Eastern (MID) AF: 0.456 AC: 134 AN: 294

European-Non Finnish (NFE) AF: 0.476 AC: 32366 AN: 67984

Other (OTH) AF: 0.441 AC: 932 AN: 2112

Alfa AF: 0.446 Hom.: 48652

Bravo AF: 0.399

Asia WGS AF: 0.320 AC: 1112 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	1.4
DANN	Benign	0.53
PhyloP100		-0.98

Splicing

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

Other links and lift over

dbSNP: rs1382269; hg19: chr3-137108482;