3-137259819-C-T

Variant names:

• chr3-137259819-C-T
• rs1382270

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 0.505 in 152,024 control chromosomes in the GnomAD database, including 21,221 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 0.51 (21221 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.619
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.67 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: 0.506 AC: 76814 AN: 151906 Hom.: 21221 Cov.: 32

Gnomad AFR AF: 0.275

Gnomad AMI AF: 0.724

Gnomad AMR AF: 0.519

Gnomad ASJ AF: 0.574

Gnomad EAS AF: 0.690

Gnomad SAS AF: 0.385

Gnomad FIN AF: 0.624

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.612

Gnomad OTH AF: 0.528

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

GnomAD4 genome AF: 0.505 AC: 76830 AN: 152024 Hom.: 21221 Cov.: 32 AF XY: 0.506 AC XY: 37629 AN XY: 74310

African (AFR) AF: 0.274 AC: 11379 AN: 41454

American (AMR) AF: 0.519 AC: 7924 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.574 AC: 1991 AN: 3468

East Asian (EAS) AF: 0.689 AC: 3561 AN: 5170

South Asian (SAS) AF: 0.385 AC: 1856 AN: 4816

European-Finnish (FIN) AF: 0.624 AC: 6597 AN: 10570

Middle Eastern (MID) AF: 0.510 AC: 148 AN: 290

European-Non Finnish (NFE) AF: 0.612 AC: 41592 AN: 67960

Other (OTH) AF: 0.532 AC: 1123 AN: 2112

Alfa AF: 0.569 Hom.: 32398

Bravo AF: 0.489

Asia WGS AF: 0.533 AC: 1852 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.98
DANN	Benign	0.70
PhyloP100		-0.62

Splicing

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

Other links and lift over

dbSNP: rs1382270; hg19: chr3-136978661;