rs4681173

Variant names:

• chr3-149459593-A-G
• rs4681173

Your query was ambiguous. Multiple possible variants found:

• chr3-149459593-A-G
• chr3-149459593-A-T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.115 in 152,232 control chromosomes in the GnomAD database, including 1,838 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 0.11 (1838 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.56
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.26).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.516 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.115 AC: 17451 AN: 152114 Hom.: 1832 Cov.: 32

Gnomad AFR AF: 0.0421

Gnomad AMI AF: 0.0791

Gnomad AMR AF: 0.148

Gnomad ASJ AF: 0.0932

Gnomad EAS AF: 0.534

Gnomad SAS AF: 0.388

Gnomad FIN AF: 0.119

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.101

Gnomad OTH AF: 0.115

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

GnomAD4 genome AF: 0.115 AC: 17475 AN: 152232 Hom.: 1838 Cov.: 32 AF XY: 0.122 AC XY: 9090 AN XY: 74422

African (AFR) AF: 0.0423 AC: 1756 AN: 41560

American (AMR) AF: 0.148 AC: 2264 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0932 AC: 323 AN: 3466

East Asian (EAS) AF: 0.533 AC: 2761 AN: 5180

South Asian (SAS) AF: 0.389 AC: 1878 AN: 4828

European-Finnish (FIN) AF: 0.119 AC: 1265 AN: 10592

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.101 AC: 6876 AN: 68002

Other (OTH) AF: 0.121 AC: 256 AN: 2114

Alfa AF: 0.110 Hom.: 4070

Bravo AF: 0.111

Asia WGS AF: 0.456 AC: 1580 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.26
CADD	Benign	15
DANN	Benign	0.83
PhyloP100		2.6

Splicing

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

Other links and lift over

dbSNP: rs4681173; hg19: chr3-149177380;