3-132954137-T-C

Position:

• chr3-132954137-T-C

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 0.593 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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.616

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
		n.132954137T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.675

Gnomad4 AMR AF: 0.553

Gnomad4 ASJ AF: 0.555

Gnomad4 EAS AF: 0.707

Gnomad4 SAS AF: 0.619

Gnomad4 FIN AF: 0.554

Gnomad4 NFE AF: 0.549

Gnomad4 OTH AF: 0.594

Alfa AF: 0.564 Hom.: 41596

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17353336; hg19: chr3-132672981;