13-45881729-A-G

Variant names:

• chr13-45881729-A-G
• rs2573294

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 0.885 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

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: 0.885 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

African (AFR) AF: 0.832 AC: 34527 AN: 41512

American (AMR) AF: 0.851 AC: 13011 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.925 AC: 3211 AN: 3470

East Asian (EAS) AF: 0.993 AC: 5156 AN: 5190

South Asian (SAS) AF: 0.929 AC: 4485 AN: 4830

European-Finnish (FIN) AF: 0.873 AC: 9255 AN: 10598

Middle Eastern (MID) AF: 0.952 AC: 280 AN: 294

European-Non Finnish (NFE) AF: 0.913 AC: 62083 AN: 68022

Other (OTH) AF: 0.888 AC: 1877 AN: 2114

Alfa AF: 0.904 Hom.: 104811

Bravo AF: 0.879

Asia WGS AF: 0.955 AC: 3321 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.5
DANN	Benign	0.76
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs2573294; hg19: chr13-46455864;