13-52823429-G-T

Position:

• chr13-52823429-G-T

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 151,950 control chromosomes in the GnomAD database, including 30,533 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 (30533 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.150

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.674 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.633 AC: 96073 AN: 151832 Hom.: 30520 Cov.: 32

Gnomad AFR AF: 0.681

Gnomad AMI AF: 0.382

Gnomad AMR AF: 0.609

Gnomad ASJ AF: 0.539

Gnomad EAS AF: 0.665

Gnomad SAS AF: 0.567

Gnomad FIN AF: 0.604

Gnomad MID AF: 0.566

Gnomad NFE AF: 0.625

Gnomad OTH AF: 0.592

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

GnomAD4 genome AF: 0.633 AC: 96131 AN: 151950 Hom.: 30533 Cov.: 32 AF XY: 0.628 AC XY: 46621 AN XY: 74256

Gnomad4 AFR AF: 0.681

Gnomad4 AMR AF: 0.609

Gnomad4 ASJ AF: 0.539

Gnomad4 EAS AF: 0.666

Gnomad4 SAS AF: 0.567

Gnomad4 FIN AF: 0.604

Gnomad4 NFE AF: 0.625

Gnomad4 OTH AF: 0.588

Alfa AF: 0.617 Hom.: 37558

Bravo AF: 0.635

Asia WGS AF: 0.604 AC: 2105 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.9
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs622348; hg19: chr13-53397564;