21-20458574-A-G

Variant names:

• chr21-20458574-A-G
• rs1786383

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 0.829 in 151,872 control chromosomes in the GnomAD database, including 52,300 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 (52300 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.549
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.88 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: 0.829 AC: 125733 AN: 151752 Hom.: 52251 Cov.: 30

Gnomad AFR AF: 0.825

Gnomad AMI AF: 0.724

Gnomad AMR AF: 0.874

Gnomad ASJ AF: 0.856

Gnomad EAS AF: 0.902

Gnomad SAS AF: 0.673

Gnomad FIN AF: 0.827

Gnomad MID AF: 0.788

Gnomad NFE AF: 0.826

Gnomad OTH AF: 0.837

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

GnomAD4 genome AF: 0.829 AC: 125842 AN: 151872 Hom.: 52300 Cov.: 30 AF XY: 0.828 AC XY: 61452 AN XY: 74214

African (AFR) AF: 0.825 AC: 34091 AN: 41310

American (AMR) AF: 0.875 AC: 13361 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.856 AC: 2972 AN: 3470

East Asian (EAS) AF: 0.902 AC: 4637 AN: 5142

South Asian (SAS) AF: 0.674 AC: 3247 AN: 4816

European-Finnish (FIN) AF: 0.827 AC: 8742 AN: 10566

Middle Eastern (MID) AF: 0.796 AC: 234 AN: 294

European-Non Finnish (NFE) AF: 0.826 AC: 56127 AN: 67974

Other (OTH) AF: 0.839 AC: 1771 AN: 2112

Alfa AF: 0.832 Hom.: 6445

Bravo AF: 0.836

Asia WGS AF: 0.806 AC: 2802 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.9
DANN	Benign	0.70
PhyloP100		0.55

Splicing

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

Other links and lift over

dbSNP: rs1786383; hg19: chr21-21830886;