rs914202

Positions:

• chr21-44981252-T-G
• chr21-44981252-T-A

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 0.804 in 152,238 control chromosomes in the GnomAD database, including 49,370 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 0.80 (49370 hom., cov: 35)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.21

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.837 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: 0.804 AC: 122349 AN: 152120 Hom.: 49330 Cov.: 35

Gnomad AFR AF: 0.837

Gnomad AMI AF: 0.750

Gnomad AMR AF: 0.817

Gnomad ASJ AF: 0.752

Gnomad EAS AF: 0.859

Gnomad SAS AF: 0.831

Gnomad FIN AF: 0.790

Gnomad MID AF: 0.775

Gnomad NFE AF: 0.782

Gnomad OTH AF: 0.801

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

GnomAD4 genome AF: 0.804 AC: 122448 AN: 152238 Hom.: 49370 Cov.: 35 AF XY: 0.804 AC XY: 59856 AN XY: 74450

Gnomad4 AFR AF: 0.837

Gnomad4 AMR AF: 0.817

Gnomad4 ASJ AF: 0.752

Gnomad4 EAS AF: 0.858

Gnomad4 SAS AF: 0.831

Gnomad4 FIN AF: 0.790

Gnomad4 NFE AF: 0.781

Gnomad4 OTH AF: 0.803

Alfa AF: 0.800 Hom.: 6070

Bravo AF: 0.805

Asia WGS AF: 0.859 AC: 2983 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.66
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs914202; hg19: chr21-46401167;