3-137259819-C-T

Position:

• chr3-137259819-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 0.505 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.274

Gnomad4 AMR AF: 0.519

Gnomad4 ASJ AF: 0.574

Gnomad4 EAS AF: 0.689

Gnomad4 SAS AF: 0.385

Gnomad4 FIN AF: 0.624

Gnomad4 NFE AF: 0.612

Gnomad4 OTH AF: 0.532

Alfa AF: 0.584 Hom.: 25885

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1382270; hg19: chr3-136978661;