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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	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

Gnomad4 AFR AF: 0.585

Gnomad4 AMR AF: 0.717

Gnomad4 ASJ AF: 0.601

Gnomad4 EAS AF: 0.831

Gnomad4 SAS AF: 0.619

Gnomad4 FIN AF: 0.703

Gnomad4 NFE AF: 0.649

Gnomad4 OTH AF: 0.666

Alfa AF: 0.650 Hom.: 48615

Bravo AF: 0.647

Asia WGS AF: 0.728 AC: 2528 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13074924; hg19: chr3-174029045;