rs2573294

chr13-45881729-A-Gchr13-45881729-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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;