chr3-117293041-T-C

Position:

• chr3-117293041-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 0.467 in 151,538 control chromosomes in the GnomAD database, including 18,565 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 0.47 (18565 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.139

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.689 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: 0.467 AC: 70709 AN: 151420 Hom.: 18550 Cov.: 31

Gnomad AFR AF: 0.696

Gnomad AMI AF: 0.274

Gnomad AMR AF: 0.397

Gnomad ASJ AF: 0.278

Gnomad EAS AF: 0.669

Gnomad SAS AF: 0.513

Gnomad FIN AF: 0.503

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.333

Gnomad OTH AF: 0.425

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

GnomAD4 genome AF: 0.467 AC: 70777 AN: 151538 Hom.: 18565 Cov.: 31 AF XY: 0.474 AC XY: 35084 AN XY: 74024

Gnomad4 AFR AF: 0.695

Gnomad4 AMR AF: 0.398

Gnomad4 ASJ AF: 0.278

Gnomad4 EAS AF: 0.668

Gnomad4 SAS AF: 0.512

Gnomad4 FIN AF: 0.503

Gnomad4 NFE AF: 0.333

Gnomad4 OTH AF: 0.426

Alfa AF: 0.356 Hom.: 7520

Bravo AF: 0.470

Asia WGS AF: 0.577 AC: 2006 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.1
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: rs1513172; hg19: chr3-117011888;