13-81872778-T-C

Variant names:

• chr13-81872778-T-C
• rs9545903

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 0.391 in 151,882 control chromosomes in the GnomAD database, including 12,161 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 0.39 (12161 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.308
• Publications: 3 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 (EAS) allele frequency at 95% confidence interval = 0.494 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.391 AC: 59337 AN: 151762 Hom.: 12148 Cov.: 31

Gnomad AFR AF: 0.262

Gnomad AMI AF: 0.366

Gnomad AMR AF: 0.345

Gnomad ASJ AF: 0.395

Gnomad EAS AF: 0.510

Gnomad SAS AF: 0.400

Gnomad FIN AF: 0.509

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.452

Gnomad OTH AF: 0.389

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

GnomAD4 genome AF: 0.391 AC: 59367 AN: 151882 Hom.: 12161 Cov.: 31 AF XY: 0.392 AC XY: 29110 AN XY: 74208

African (AFR) AF: 0.262 AC: 10866 AN: 41422

American (AMR) AF: 0.344 AC: 5261 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.395 AC: 1368 AN: 3460

East Asian (EAS) AF: 0.510 AC: 2618 AN: 5132

South Asian (SAS) AF: 0.401 AC: 1929 AN: 4812

European-Finnish (FIN) AF: 0.509 AC: 5361 AN: 10536

Middle Eastern (MID) AF: 0.401 AC: 118 AN: 294

European-Non Finnish (NFE) AF: 0.452 AC: 30687 AN: 67930

Other (OTH) AF: 0.391 AC: 826 AN: 2110

Alfa AF: 0.426 Hom.: 7943

Bravo AF: 0.373

Asia WGS AF: 0.458 AC: 1591 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	7.5
DANN	Benign	0.79
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs9545903; hg19: chr13-82446913;