13-72328053-T-C

Variant names:

• chr13-72328053-T-C
• rs490599

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 0.359 in 151,886 control chromosomes in the GnomAD database, including 10,057 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 0.36 (10057 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0880

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 (SAS) allele frequency at 95% confidence interval = 0.503 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: 0.359 AC: 54445 AN: 151768 Hom.: 10036 Cov.: 32

Gnomad AFR AF: 0.401

Gnomad AMI AF: 0.492

Gnomad AMR AF: 0.351

Gnomad ASJ AF: 0.354

Gnomad EAS AF: 0.318

Gnomad SAS AF: 0.520

Gnomad FIN AF: 0.359

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.324

Gnomad OTH AF: 0.368

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

GnomAD4 genome AF: 0.359 AC: 54523 AN: 151886 Hom.: 10057 Cov.: 32 AF XY: 0.364 AC XY: 27049 AN XY: 74266

Gnomad4 AFR AF: 0.401

Gnomad4 AMR AF: 0.352

Gnomad4 ASJ AF: 0.354

Gnomad4 EAS AF: 0.318

Gnomad4 SAS AF: 0.520

Gnomad4 FIN AF: 0.359

Gnomad4 NFE AF: 0.324

Gnomad4 OTH AF: 0.371

Alfa AF: 0.327 Hom.: 1678

Bravo AF: 0.356

Asia WGS AF: 0.437 AC: 1524 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	4.1
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs490599; hg19: chr13-72902191; COSMIC: COSV69363280;