21-32059682-A-G

Position:

• chr21-32059682-A-G

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 0.327 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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	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

Gnomad4 AFR AF: 0.294

Gnomad4 AMR AF: 0.306

Gnomad4 ASJ AF: 0.176

Gnomad4 EAS AF: 0.371

Gnomad4 SAS AF: 0.302

Gnomad4 FIN AF: 0.423

Gnomad4 NFE AF: 0.347

Gnomad4 OTH AF: 0.289

Alfa AF: 0.327 Hom.: 13401

Bravo AF: 0.315

Asia WGS AF: 0.328 AC: 1140 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1892577; hg19: chr21-33431995;