3-132954137-T-C

Variant names:

• chr3-132954137-T-C
• rs17353336

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 0.593 in 151,774 control chromosomes in the GnomAD database, including 26,899 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 0.59 (26899 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.616
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.688 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: 0.593 AC: 89960 AN: 151656 Hom.: 26885 Cov.: 30

Gnomad AFR AF: 0.676

Gnomad AMI AF: 0.577

Gnomad AMR AF: 0.553

Gnomad ASJ AF: 0.555

Gnomad EAS AF: 0.708

Gnomad SAS AF: 0.620

Gnomad FIN AF: 0.554

Gnomad MID AF: 0.736

Gnomad NFE AF: 0.549

Gnomad OTH AF: 0.595

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

GnomAD4 genome AF: 0.593 AC: 90004 AN: 151774 Hom.: 26899 Cov.: 30 AF XY: 0.594 AC XY: 44072 AN XY: 74166

African (AFR) AF: 0.675 AC: 27936 AN: 41370

American (AMR) AF: 0.553 AC: 8440 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.555 AC: 1922 AN: 3464

East Asian (EAS) AF: 0.707 AC: 3636 AN: 5140

South Asian (SAS) AF: 0.619 AC: 2962 AN: 4786

European-Finnish (FIN) AF: 0.554 AC: 5840 AN: 10550

Middle Eastern (MID) AF: 0.736 AC: 215 AN: 292

European-Non Finnish (NFE) AF: 0.549 AC: 37277 AN: 67894

Other (OTH) AF: 0.594 AC: 1253 AN: 2108

Alfa AF: 0.567 Hom.: 94673

Bravo AF: 0.599

Asia WGS AF: 0.670 AC: 2328 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.6
DANN	Benign	0.76
PhyloP100		-0.62

Splicing

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

Other links and lift over

dbSNP: rs17353336; hg19: chr3-132672981;