rs13052596

Variant names:

• chr21-42351407-C-A
• rs13052596

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 0.276 in 152,020 control chromosomes in the GnomAD database, including 6,150 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 0.28 (6150 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.693

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.33 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: 0.277 AC: 42021 AN: 151902 Hom.: 6149 Cov.: 32

Gnomad AFR AF: 0.189

Gnomad AMI AF: 0.319

Gnomad AMR AF: 0.249

Gnomad ASJ AF: 0.298

Gnomad EAS AF: 0.343

Gnomad SAS AF: 0.332

Gnomad FIN AF: 0.294

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.322

Gnomad OTH AF: 0.288

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

GnomAD4 genome AF: 0.276 AC: 42029 AN: 152020 Hom.: 6150 Cov.: 32 AF XY: 0.278 AC XY: 20623 AN XY: 74312

Gnomad4 AFR AF: 0.189

Gnomad4 AMR AF: 0.249

Gnomad4 ASJ AF: 0.298

Gnomad4 EAS AF: 0.343

Gnomad4 SAS AF: 0.332

Gnomad4 FIN AF: 0.294

Gnomad4 NFE AF: 0.322

Gnomad4 OTH AF: 0.286

Alfa AF: 0.283 Hom.: 790

Bravo AF: 0.268

Asia WGS AF: 0.316 AC: 1096 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.9
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13052596; hg19: chr21-43771516;