rs726540

chr13-52834269-T-G

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;