chr21-19594402-A-G

Variant names:

• chr21-19594402-A-G
• rs2825673

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 0.201 in 151,986 control chromosomes in the GnomAD database, including 3,813 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 0.20 (3813 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.647

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.339 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: 0.201 AC: 30486 AN: 151868 Hom.: 3816 Cov.: 32

Gnomad AFR AF: 0.343

Gnomad AMI AF: 0.280

Gnomad AMR AF: 0.128

Gnomad ASJ AF: 0.176

Gnomad EAS AF: 0.246

Gnomad SAS AF: 0.238

Gnomad FIN AF: 0.140

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.134

Gnomad OTH AF: 0.197

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

GnomAD4 genome AF: 0.201 AC: 30519 AN: 151986 Hom.: 3813 Cov.: 32 AF XY: 0.200 AC XY: 14895 AN XY: 74298

Gnomad4 AFR AF: 0.343

Gnomad4 AMR AF: 0.128

Gnomad4 ASJ AF: 0.176

Gnomad4 EAS AF: 0.246

Gnomad4 SAS AF: 0.239

Gnomad4 FIN AF: 0.140

Gnomad4 NFE AF: 0.134

Gnomad4 OTH AF: 0.199

Alfa AF: 0.139 Hom.: 2380

Bravo AF: 0.205

Asia WGS AF: 0.234 AC: 812 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.73
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2825673; hg19: chr21-20966716;