3-57994040-G-T

Position:

• chr3-57994040-G-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 0.762 in 151,868 control chromosomes in the GnomAD database, including 44,836 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 0.76 (44836 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.762

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.93 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: 0.762 AC: 115624 AN: 151750 Hom.: 44792 Cov.: 29

Gnomad AFR AF: 0.866

Gnomad AMI AF: 0.683

Gnomad AMR AF: 0.763

Gnomad ASJ AF: 0.874

Gnomad EAS AF: 0.952

Gnomad SAS AF: 0.858

Gnomad FIN AF: 0.694

Gnomad MID AF: 0.854

Gnomad NFE AF: 0.682

Gnomad OTH AF: 0.779

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

GnomAD4 genome AF: 0.762 AC: 115723 AN: 151868 Hom.: 44836 Cov.: 29 AF XY: 0.768 AC XY: 56956 AN XY: 74184

Gnomad4 AFR AF: 0.866

Gnomad4 AMR AF: 0.764

Gnomad4 ASJ AF: 0.874

Gnomad4 EAS AF: 0.952

Gnomad4 SAS AF: 0.858

Gnomad4 FIN AF: 0.694

Gnomad4 NFE AF: 0.682

Gnomad4 OTH AF: 0.780

Alfa AF: 0.716 Hom.: 22768

Bravo AF: 0.773

Asia WGS AF: 0.888 AC: 3090 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	3.5
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1098018; hg19: chr3-57979767;