rs2373154

Variant names:

• chr3-46129606-G-A
• rs2373154

Your query was ambiguous. Multiple possible variants found:

• chr3-46129606-G-A
• chr3-46129606-G-C
• chr3-46129606-G-T

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 0.401 in 151,874 control chromosomes in the GnomAD database, including 13,040 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 0.40 (13040 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.10
• Publications: 11 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.644 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.401 AC: 60863 AN: 151756 Hom.: 13015 Cov.: 30

Gnomad AFR AF: 0.263

Gnomad AMI AF: 0.356

Gnomad AMR AF: 0.499

Gnomad ASJ AF: 0.374

Gnomad EAS AF: 0.664

Gnomad SAS AF: 0.376

Gnomad FIN AF: 0.459

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.438

Gnomad OTH AF: 0.395

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

GnomAD4 genome AF: 0.401 AC: 60935 AN: 151874 Hom.: 13040 Cov.: 30 AF XY: 0.404 AC XY: 30007 AN XY: 74210

African (AFR) AF: 0.263 AC: 10890 AN: 41390

American (AMR) AF: 0.500 AC: 7632 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.374 AC: 1297 AN: 3464

East Asian (EAS) AF: 0.663 AC: 3413 AN: 5148

South Asian (SAS) AF: 0.376 AC: 1812 AN: 4824

European-Finnish (FIN) AF: 0.459 AC: 4841 AN: 10548

Middle Eastern (MID) AF: 0.347 AC: 102 AN: 294

European-Non Finnish (NFE) AF: 0.438 AC: 29779 AN: 67930

Other (OTH) AF: 0.401 AC: 845 AN: 2108

Alfa AF: 0.420 Hom.: 9833

Bravo AF: 0.396

Asia WGS AF: 0.524 AC: 1820 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.97
DANN	Benign	0.29
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs2373154; hg19: chr3-46171098;