rs13050454

Variant names:

• chr21-26334004-G-A
• rs13050454

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 0.34 in 152,070 control chromosomes in the GnomAD database, including 9,838 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 0.34 (9838 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.223

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.406 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: 0.340 AC: 51646 AN: 151954 Hom.: 9833 Cov.: 32

Gnomad AFR AF: 0.152

Gnomad AMI AF: 0.419

Gnomad AMR AF: 0.382

Gnomad ASJ AF: 0.434

Gnomad EAS AF: 0.367

Gnomad SAS AF: 0.418

Gnomad FIN AF: 0.472

Gnomad MID AF: 0.420

Gnomad NFE AF: 0.410

Gnomad OTH AF: 0.358

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

GnomAD4 genome AF: 0.340 AC: 51662 AN: 152070 Hom.: 9838 Cov.: 32 AF XY: 0.345 AC XY: 25618 AN XY: 74314

Gnomad4 AFR AF: 0.151

Gnomad4 AMR AF: 0.382

Gnomad4 ASJ AF: 0.434

Gnomad4 EAS AF: 0.367

Gnomad4 SAS AF: 0.418

Gnomad4 FIN AF: 0.472

Gnomad4 NFE AF: 0.410

Gnomad4 OTH AF: 0.362

Alfa AF: 0.402 Hom.: 15691

Bravo AF: 0.324

Asia WGS AF: 0.396 AC: 1377 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.4
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13050454; hg19: chr21-27706323;