21-19824828-C-G

Variant names:

• chr21-19824828-C-G
• rs2825825

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.671 AC: 27779 AN: 41412

American (AMR) AF: 0.875 AC: 13380 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.955 AC: 3315 AN: 3470

East Asian (EAS) AF: 0.968 AC: 5008 AN: 5176

South Asian (SAS) AF: 0.907 AC: 4379 AN: 4826

European-Finnish (FIN) AF: 0.888 AC: 9410 AN: 10594

Middle Eastern (MID) AF: 0.861 AC: 253 AN: 294

European-Non Finnish (NFE) AF: 0.890 AC: 60523 AN: 68020

Other (OTH) AF: 0.845 AC: 1785 AN: 2112

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
PhyloP100		-0.078

Splicing

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

Other links and lift over

dbSNP: rs2825825; hg19: chr21-21197142;