3-57994040-G-T

Variant names:

• chr3-57994040-G-T
• rs1098018

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.866 AC: 35908 AN: 41462

American (AMR) AF: 0.764 AC: 11626 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.874 AC: 3033 AN: 3472

East Asian (EAS) AF: 0.952 AC: 4919 AN: 5166

South Asian (SAS) AF: 0.858 AC: 4115 AN: 4798

European-Finnish (FIN) AF: 0.694 AC: 7298 AN: 10516

Middle Eastern (MID) AF: 0.864 AC: 254 AN: 294

European-Non Finnish (NFE) AF: 0.682 AC: 46311 AN: 67926

Other (OTH) AF: 0.780 AC: 1639 AN: 2100

Alfa AF: 0.718 Hom.: 25042

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
PhyloP100		0.76

Splicing

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

Other links and lift over

dbSNP: rs1098018; hg19: chr3-57979767;