21-19824828-C-G

Position:

• chr21-19824828-C-G

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 152,106 control chromosomes in the GnomAD database, including 53,489 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 (53489 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0780

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• 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/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.833 AC: 126578 AN: 151988 Hom.: 53455 Cov.: 32

Gnomad AFR AF: 0.671

Gnomad AMI AF: 0.911

Gnomad AMR AF: 0.875

Gnomad ASJ AF: 0.955

Gnomad EAS AF: 0.968

Gnomad SAS AF: 0.907

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: 126663 AN: 152106 Hom.: 53489 Cov.: 32 AF XY: 0.835 AC XY: 62098 AN XY: 74370

Gnomad4 AFR AF: 0.671

Gnomad4 AMR AF: 0.875

Gnomad4 ASJ AF: 0.955

Gnomad4 EAS AF: 0.968

Gnomad4 SAS AF: 0.907

Gnomad4 FIN AF: 0.888

Gnomad4 NFE AF: 0.890

Gnomad4 OTH AF: 0.845

Alfa AF: 0.815 Hom.: 1957

Bravo AF: 0.827

Asia WGS AF: 0.903 AC: 3137 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.0
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2825825; hg19: chr21-21197142;