3-114119743-T-A

Position:

• chr3-114119743-T-A

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 0.913 in 152,262 control chromosomes in the GnomAD database, including 64,082 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 0.91 (64082 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.485

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.966 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: 0.913 AC: 138880 AN: 152144 Hom.: 64067 Cov.: 32

Gnomad AFR AF: 0.762

Gnomad AMI AF: 0.974

Gnomad AMR AF: 0.956

Gnomad ASJ AF: 0.985

Gnomad EAS AF: 0.978

Gnomad SAS AF: 0.939

Gnomad FIN AF: 0.979

Gnomad MID AF: 0.962

Gnomad NFE AF: 0.972

Gnomad OTH AF: 0.933

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

GnomAD4 genome AF: 0.913 AC: 138940 AN: 152262 Hom.: 64082 Cov.: 32 AF XY: 0.914 AC XY: 68074 AN XY: 74448

Gnomad4 AFR AF: 0.762

Gnomad4 AMR AF: 0.956

Gnomad4 ASJ AF: 0.985

Gnomad4 EAS AF: 0.978

Gnomad4 SAS AF: 0.939

Gnomad4 FIN AF: 0.979

Gnomad4 NFE AF: 0.972

Gnomad4 OTH AF: 0.933

Alfa AF: 0.937 Hom.: 8348

Bravo AF: 0.907

Asia WGS AF: 0.946 AC: 3289 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	7.1
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6808291; hg19: chr3-113838590;