rs2573294

Variant names:

• chr13-45881729-A-G
• rs2573294

Your query was ambiguous. Multiple possible variants found:

• chr13-45881729-A-G
• chr13-45881729-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 0.885 in 152,240 control chromosomes in the GnomAD database, including 59,737 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 0.88 (59737 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.135

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.971 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: 0.885 AC: 134575 AN: 152120 Hom.: 59685 Cov.: 33

Gnomad AFR AF: 0.831

Gnomad AMI AF: 0.877

Gnomad AMR AF: 0.851

Gnomad ASJ AF: 0.925

Gnomad EAS AF: 0.993

Gnomad SAS AF: 0.928

Gnomad FIN AF: 0.873

Gnomad MID AF: 0.953

Gnomad NFE AF: 0.913

Gnomad OTH AF: 0.887

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

GnomAD4 genome AF: 0.885 AC: 134685 AN: 152240 Hom.: 59737 Cov.: 33 AF XY: 0.883 AC XY: 65699 AN XY: 74414

Gnomad4 AFR AF: 0.832

Gnomad4 AMR AF: 0.851

Gnomad4 ASJ AF: 0.925

Gnomad4 EAS AF: 0.993

Gnomad4 SAS AF: 0.929

Gnomad4 FIN AF: 0.873

Gnomad4 NFE AF: 0.913

Gnomad4 OTH AF: 0.888

Alfa AF: 0.908 Hom.: 83117

Bravo AF: 0.879

Asia WGS AF: 0.955 AC: 3321 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.5
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2573294; hg19: chr13-46455864;