21-19824294-C-G

Variant names:

• chr21-19824294-C-G
• rs2825822

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 0.833 in 151,942 control chromosomes in the GnomAD database, including 53,444 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 0.83 (53444 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.505

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.945 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: 0.833 AC: 126451 AN: 151824 Hom.: 53411 Cov.: 30

Gnomad AFR AF: 0.671

Gnomad AMI AF: 0.913

Gnomad AMR AF: 0.875

Gnomad ASJ AF: 0.955

Gnomad EAS AF: 0.967

Gnomad SAS AF: 0.908

Gnomad FIN AF: 0.888

Gnomad MID AF: 0.861

Gnomad NFE AF: 0.890

Gnomad OTH AF: 0.845

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

GnomAD4 genome AF: 0.833 AC: 126534 AN: 151942 Hom.: 53444 Cov.: 30 AF XY: 0.835 AC XY: 62010 AN XY: 74244

Gnomad4 AFR AF: 0.671

Gnomad4 AMR AF: 0.875

Gnomad4 ASJ AF: 0.955

Gnomad4 EAS AF: 0.967

Gnomad4 SAS AF: 0.907

Gnomad4 FIN AF: 0.888

Gnomad4 NFE AF: 0.890

Gnomad4 OTH AF: 0.845

Alfa AF: 0.841 Hom.: 2830

Bravo AF: 0.826

Asia WGS AF: 0.903 AC: 3139 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	1.5
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: rs2825822; hg19: chr21-21196608;