rs726540

Variant names:

• chr13-52834269-T-G
• rs726540

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 0.633 in 152,018 control chromosomes in the GnomAD database, including 30,646 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 0.63 (30646 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.213

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.776 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: 0.633 AC: 96130 AN: 151900 Hom.: 30623 Cov.: 32

Gnomad AFR AF: 0.565

Gnomad AMI AF: 0.708

Gnomad AMR AF: 0.685

Gnomad ASJ AF: 0.569

Gnomad EAS AF: 0.797

Gnomad SAS AF: 0.581

Gnomad FIN AF: 0.752

Gnomad MID AF: 0.598

Gnomad NFE AF: 0.637

Gnomad OTH AF: 0.646

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

GnomAD4 genome AF: 0.633 AC: 96202 AN: 152018 Hom.: 30646 Cov.: 32 AF XY: 0.641 AC XY: 47630 AN XY: 74308

Gnomad4 AFR AF: 0.566

Gnomad4 AMR AF: 0.685

Gnomad4 ASJ AF: 0.569

Gnomad4 EAS AF: 0.796

Gnomad4 SAS AF: 0.581

Gnomad4 FIN AF: 0.752

Gnomad4 NFE AF: 0.637

Gnomad4 OTH AF: 0.648

Alfa AF: 0.637 Hom.: 53857

Bravo AF: 0.627

Asia WGS AF: 0.688 AC: 2391 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	3.1
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs726540; hg19: chr13-53408404;