3-106139483-T-G

Variant names:

• chr3-106139483-T-G
• rs1373737

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 0.623 in 151,986 control chromosomes in the GnomAD database, including 30,044 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 0.62 (30044 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.26
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.797 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.623 AC: 94606 AN: 151868 Hom.: 30049 Cov.: 32

Gnomad AFR AF: 0.516

Gnomad AMI AF: 0.538

Gnomad AMR AF: 0.688

Gnomad ASJ AF: 0.711

Gnomad EAS AF: 0.818

Gnomad SAS AF: 0.508

Gnomad FIN AF: 0.741

Gnomad MID AF: 0.668

Gnomad NFE AF: 0.645

Gnomad OTH AF: 0.638

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

GnomAD4 genome AF: 0.623 AC: 94626 AN: 151986 Hom.: 30044 Cov.: 32 AF XY: 0.626 AC XY: 46490 AN XY: 74296

African (AFR) AF: 0.515 AC: 21352 AN: 41468

American (AMR) AF: 0.688 AC: 10515 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.711 AC: 2463 AN: 3466

East Asian (EAS) AF: 0.817 AC: 4227 AN: 5172

South Asian (SAS) AF: 0.507 AC: 2446 AN: 4824

European-Finnish (FIN) AF: 0.741 AC: 7807 AN: 10542

Middle Eastern (MID) AF: 0.680 AC: 200 AN: 294

European-Non Finnish (NFE) AF: 0.645 AC: 43790 AN: 67914

Other (OTH) AF: 0.633 AC: 1335 AN: 2110

Alfa AF: 0.636 Hom.: 5216

Bravo AF: 0.620

Asia WGS AF: 0.609 AC: 2094 AN: 3440

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.8
DANN	Benign	0.45
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs1373737; hg19: chr3-105858330;