chr21-30011979-A-G

Variant names:

• chr21-30011979-A-G
• rs2832533

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 0.604 in 151,868 control chromosomes in the GnomAD database, including 30,423 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 0.60 (30423 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.69
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.749 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: 0.604 AC: 91624 AN: 151748 Hom.: 30425 Cov.: 31

Gnomad AFR AF: 0.336

Gnomad AMI AF: 0.816

Gnomad AMR AF: 0.564

Gnomad ASJ AF: 0.712

Gnomad EAS AF: 0.501

Gnomad SAS AF: 0.490

Gnomad FIN AF: 0.777

Gnomad MID AF: 0.652

Gnomad NFE AF: 0.754

Gnomad OTH AF: 0.635

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

GnomAD4 genome AF: 0.604 AC: 91654 AN: 151868 Hom.: 30423 Cov.: 31 AF XY: 0.601 AC XY: 44645 AN XY: 74224

African (AFR) AF: 0.336 AC: 13916 AN: 41374

American (AMR) AF: 0.563 AC: 8587 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.712 AC: 2468 AN: 3466

East Asian (EAS) AF: 0.502 AC: 2588 AN: 5156

South Asian (SAS) AF: 0.491 AC: 2362 AN: 4806

European-Finnish (FIN) AF: 0.777 AC: 8197 AN: 10552

Middle Eastern (MID) AF: 0.646 AC: 190 AN: 294

European-Non Finnish (NFE) AF: 0.754 AC: 51268 AN: 67954

Other (OTH) AF: 0.633 AC: 1335 AN: 2108

Alfa AF: 0.650 Hom.: 13395

Bravo AF: 0.575

Asia WGS AF: 0.502 AC: 1748 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.26
DANN	Benign	0.58
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs2832533; hg19: chr21-31384297;