3-138135633-A-G

Variant names:

• chr3-138135633-A-G
• rs2346747

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 0.544 in 152,046 control chromosomes in the GnomAD database, including 25,003 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 0.54 (25003 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.210
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.661 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: 0.544 AC: 82640 AN: 151928 Hom.: 25002 Cov.: 32

Gnomad AFR AF: 0.255

Gnomad AMI AF: 0.477

Gnomad AMR AF: 0.649

Gnomad ASJ AF: 0.685

Gnomad EAS AF: 0.579

Gnomad SAS AF: 0.594

Gnomad FIN AF: 0.645

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.666

Gnomad OTH AF: 0.588

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

GnomAD4 genome AF: 0.544 AC: 82661 AN: 152046 Hom.: 25003 Cov.: 32 AF XY: 0.546 AC XY: 40595 AN XY: 74308

African (AFR) AF: 0.254 AC: 10561 AN: 41500

American (AMR) AF: 0.649 AC: 9915 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.685 AC: 2376 AN: 3470

East Asian (EAS) AF: 0.579 AC: 2987 AN: 5160

South Asian (SAS) AF: 0.596 AC: 2872 AN: 4818

European-Finnish (FIN) AF: 0.645 AC: 6808 AN: 10552

Middle Eastern (MID) AF: 0.636 AC: 187 AN: 294

European-Non Finnish (NFE) AF: 0.666 AC: 45291 AN: 67956

Other (OTH) AF: 0.583 AC: 1230 AN: 2110

Alfa AF: 0.450 Hom.: 1347

Bravo AF: 0.532

Asia WGS AF: 0.534 AC: 1862 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	7.3
DANN	Benign	0.70
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs2346747; hg19: chr3-137854475;