3-179633577-C-T

Position:

• chr3-179633577-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 0.568 in 152,100 control chromosomes in the GnomAD database, including 25,430 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 0.57 (25430 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.11

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.751 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: 0.569 AC: 86410 AN: 151982 Hom.: 25425 Cov.: 32

Gnomad AFR AF: 0.398

Gnomad AMI AF: 0.740

Gnomad AMR AF: 0.626

Gnomad ASJ AF: 0.666

Gnomad EAS AF: 0.771

Gnomad SAS AF: 0.668

Gnomad FIN AF: 0.605

Gnomad MID AF: 0.665

Gnomad NFE AF: 0.622

Gnomad OTH AF: 0.632

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

GnomAD4 genome AF: 0.568 AC: 86455 AN: 152100 Hom.: 25430 Cov.: 32 AF XY: 0.575 AC XY: 42725 AN XY: 74362

Gnomad4 AFR AF: 0.398

Gnomad4 AMR AF: 0.626

Gnomad4 ASJ AF: 0.666

Gnomad4 EAS AF: 0.771

Gnomad4 SAS AF: 0.667

Gnomad4 FIN AF: 0.605

Gnomad4 NFE AF: 0.622

Gnomad4 OTH AF: 0.635

Alfa AF: 0.597 Hom.: 5671

Bravo AF: 0.562

Asia WGS AF: 0.678 AC: 2357 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.52
DANN	Benign	0.21

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6443662; hg19: chr3-179351365;