13-81872778-T-C

Variant names:

• chr13-81872778-T-C
• rs9545903

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 0.391 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.391 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

Gnomad4 AFR AF: 0.262

Gnomad4 AMR AF: 0.344

Gnomad4 ASJ AF: 0.395

Gnomad4 EAS AF: 0.510

Gnomad4 SAS AF: 0.401

Gnomad4 FIN AF: 0.509

Gnomad4 NFE AF: 0.452

Gnomad4 OTH AF: 0.391

Alfa AF: 0.427 Hom.: 7160

Bravo AF: 0.373

Asia WGS AF: 0.458 AC: 1591 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9545903; hg19: chr13-82446913;