rs1792040

Variant names:

• chr13-28802806-A-G
• rs1792040

Your query was ambiguous. Multiple possible variants found:

• chr13-28802806-A-G
• chr13-28802806-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 0.815 in 152,232 control chromosomes in the GnomAD database, including 51,124 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 0.82 (51124 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.390
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.85 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: 0.815 AC: 124016 AN: 152114 Hom.: 51064 Cov.: 33

Gnomad AFR AF: 0.857

Gnomad AMI AF: 0.586

Gnomad AMR AF: 0.834

Gnomad ASJ AF: 0.835

Gnomad EAS AF: 0.533

Gnomad SAS AF: 0.566

Gnomad FIN AF: 0.842

Gnomad MID AF: 0.816

Gnomad NFE AF: 0.823

Gnomad OTH AF: 0.810

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

GnomAD4 genome AF: 0.815 AC: 124137 AN: 152232 Hom.: 51124 Cov.: 33 AF XY: 0.812 AC XY: 60448 AN XY: 74436

African (AFR) AF: 0.858 AC: 35627 AN: 41536

American (AMR) AF: 0.834 AC: 12755 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.835 AC: 2897 AN: 3470

East Asian (EAS) AF: 0.532 AC: 2747 AN: 5160

South Asian (SAS) AF: 0.565 AC: 2730 AN: 4828

European-Finnish (FIN) AF: 0.842 AC: 8929 AN: 10608

Middle Eastern (MID) AF: 0.827 AC: 243 AN: 294

European-Non Finnish (NFE) AF: 0.823 AC: 55970 AN: 68018

Other (OTH) AF: 0.808 AC: 1706 AN: 2112

Alfa AF: 0.837 Hom.: 6545

Bravo AF: 0.822

Asia WGS AF: 0.569 AC: 1980 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.9
DANN	Benign	0.86
PhyloP100		-0.39

Splicing

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

Other links and lift over

dbSNP: rs1792040; hg19: chr13-29376943;