rs13074924

Variant names:

• chr3-174311255-A-G
• rs13074924

Your query was ambiguous. Multiple possible variants found:

• chr3-174311255-A-G
• chr3-174311255-A-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 0.647 in 151,914 control chromosomes in the GnomAD database, including 32,058 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 0.65 (32058 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0880
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.811 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: 0.647 AC: 98157 AN: 151796 Hom.: 32040 Cov.: 32

Gnomad AFR AF: 0.585

Gnomad AMI AF: 0.678

Gnomad AMR AF: 0.717

Gnomad ASJ AF: 0.601

Gnomad EAS AF: 0.831

Gnomad SAS AF: 0.620

Gnomad FIN AF: 0.703

Gnomad MID AF: 0.601

Gnomad NFE AF: 0.649

Gnomad OTH AF: 0.663

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

GnomAD4 genome AF: 0.647 AC: 98231 AN: 151914 Hom.: 32058 Cov.: 32 AF XY: 0.649 AC XY: 48237 AN XY: 74272

African (AFR) AF: 0.585 AC: 24209 AN: 41404

American (AMR) AF: 0.717 AC: 10926 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.601 AC: 2087 AN: 3472

East Asian (EAS) AF: 0.831 AC: 4285 AN: 5154

South Asian (SAS) AF: 0.619 AC: 2977 AN: 4812

European-Finnish (FIN) AF: 0.703 AC: 7428 AN: 10562

Middle Eastern (MID) AF: 0.595 AC: 175 AN: 294

European-Non Finnish (NFE) AF: 0.649 AC: 44126 AN: 67954

Other (OTH) AF: 0.666 AC: 1402 AN: 2106

Alfa AF: 0.650 Hom.: 77116

Bravo AF: 0.647

Asia WGS AF: 0.728 AC: 2528 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.7
DANN	Benign	0.66
PhyloP100		0.088

Splicing

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

Other links and lift over

dbSNP: rs13074924; hg19: chr3-174029045;