21-19728555-A-G

Variant names:

• chr21-19728555-A-G
• rs2825761

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 0.57 in 151,692 control chromosomes in the GnomAD database, including 24,918 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 0.57 (24918 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.571
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.619 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.570 AC: 86398 AN: 151574 Hom.: 24905 Cov.: 30

Gnomad AFR AF: 0.520

Gnomad AMI AF: 0.729

Gnomad AMR AF: 0.525

Gnomad ASJ AF: 0.474

Gnomad EAS AF: 0.467

Gnomad SAS AF: 0.430

Gnomad FIN AF: 0.613

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.624

Gnomad OTH AF: 0.586

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

GnomAD4 genome AF: 0.570 AC: 86455 AN: 151692 Hom.: 24918 Cov.: 30 AF XY: 0.565 AC XY: 41882 AN XY: 74102

African (AFR) AF: 0.520 AC: 21512 AN: 41338

American (AMR) AF: 0.525 AC: 7998 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.474 AC: 1644 AN: 3466

East Asian (EAS) AF: 0.467 AC: 2401 AN: 5144

South Asian (SAS) AF: 0.430 AC: 2061 AN: 4792

European-Finnish (FIN) AF: 0.613 AC: 6430 AN: 10492

Middle Eastern (MID) AF: 0.551 AC: 161 AN: 292

European-Non Finnish (NFE) AF: 0.624 AC: 42345 AN: 67902

Other (OTH) AF: 0.587 AC: 1238 AN: 2110

Alfa AF: 0.588 Hom.: 3182

Bravo AF: 0.562

Asia WGS AF: 0.437 AC: 1516 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.4
DANN	Benign	0.66
PhyloP100		-0.57

Splicing

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

Other links and lift over

dbSNP: rs2825761; hg19: chr21-21100869;