21-32059682-A-G

Variant names:

• chr21-32059682-A-G
• rs1892577

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 0.327 in 151,924 control chromosomes in the GnomAD database, including 8,460 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 0.33 (8460 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.432
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.357 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: 0.327 AC: 49676 AN: 151806 Hom.: 8452 Cov.: 31

Gnomad AFR AF: 0.294

Gnomad AMI AF: 0.217

Gnomad AMR AF: 0.306

Gnomad ASJ AF: 0.176

Gnomad EAS AF: 0.371

Gnomad SAS AF: 0.301

Gnomad FIN AF: 0.423

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.347

Gnomad OTH AF: 0.285

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

GnomAD4 genome AF: 0.327 AC: 49704 AN: 151924 Hom.: 8460 Cov.: 31 AF XY: 0.328 AC XY: 24342 AN XY: 74248

African (AFR) AF: 0.294 AC: 12177 AN: 41428

American (AMR) AF: 0.306 AC: 4675 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.176 AC: 610 AN: 3468

East Asian (EAS) AF: 0.371 AC: 1910 AN: 5150

South Asian (SAS) AF: 0.302 AC: 1450 AN: 4804

European-Finnish (FIN) AF: 0.423 AC: 4460 AN: 10538

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.347 AC: 23576 AN: 67948

Other (OTH) AF: 0.289 AC: 609 AN: 2110

Alfa AF: 0.332 Hom.: 32749

Bravo AF: 0.315

Asia WGS AF: 0.328 AC: 1140 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.8
DANN	Benign	0.66
PhyloP100		0.43

Splicing

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

Other links and lift over

dbSNP: rs1892577; hg19: chr21-33431995;