3-138849749-A-G

Variant names:

• chr3-138849749-A-G
• rs7613579

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 0.582 in 151,986 control chromosomes in the GnomAD database, including 26,545 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 0.58 (26545 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.554
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.963 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: 0.582 AC: 88365 AN: 151868 Hom.: 26515 Cov.: 32

Gnomad AFR AF: 0.561

Gnomad AMI AF: 0.505

Gnomad AMR AF: 0.648

Gnomad ASJ AF: 0.469

Gnomad EAS AF: 0.986

Gnomad SAS AF: 0.662

Gnomad FIN AF: 0.669

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.537

Gnomad OTH AF: 0.556

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

GnomAD4 genome AF: 0.582 AC: 88450 AN: 151986 Hom.: 26545 Cov.: 32 AF XY: 0.595 AC XY: 44177 AN XY: 74286

African (AFR) AF: 0.561 AC: 23269 AN: 41454

American (AMR) AF: 0.649 AC: 9893 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.469 AC: 1625 AN: 3466

East Asian (EAS) AF: 0.986 AC: 5090 AN: 5162

South Asian (SAS) AF: 0.662 AC: 3186 AN: 4814

European-Finnish (FIN) AF: 0.669 AC: 7076 AN: 10572

Middle Eastern (MID) AF: 0.476 AC: 140 AN: 294

European-Non Finnish (NFE) AF: 0.537 AC: 36527 AN: 67964

Other (OTH) AF: 0.562 AC: 1184 AN: 2108

Alfa AF: 0.547 Hom.: 29048

Bravo AF: 0.582

Asia WGS AF: 0.810 AC: 2815 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.5
DANN	Benign	0.74
PhyloP100		0.55

Splicing

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

Other links and lift over

dbSNP: rs7613579; hg19: chr3-138568591;