21-17414857-G-A

Variant names:

• chr21-17414857-G-A
• rs2824292

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 0.476 in 151,884 control chromosomes in the GnomAD database, including 18,067 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 0.48 (18067 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0890
• Publications: 22 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.573 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: 0.476 AC: 72220 AN: 151766 Hom.: 18069 Cov.: 31

Gnomad AFR AF: 0.314

Gnomad AMI AF: 0.542

Gnomad AMR AF: 0.509

Gnomad ASJ AF: 0.558

Gnomad EAS AF: 0.450

Gnomad SAS AF: 0.592

Gnomad FIN AF: 0.560

Gnomad MID AF: 0.490

Gnomad NFE AF: 0.543

Gnomad OTH AF: 0.479

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

GnomAD4 genome AF: 0.476 AC: 72262 AN: 151884 Hom.: 18067 Cov.: 31 AF XY: 0.481 AC XY: 35685 AN XY: 74224

African (AFR) AF: 0.314 AC: 12995 AN: 41432

American (AMR) AF: 0.509 AC: 7759 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.558 AC: 1933 AN: 3466

East Asian (EAS) AF: 0.450 AC: 2320 AN: 5152

South Asian (SAS) AF: 0.591 AC: 2844 AN: 4810

European-Finnish (FIN) AF: 0.560 AC: 5883 AN: 10514

Middle Eastern (MID) AF: 0.486 AC: 142 AN: 292

European-Non Finnish (NFE) AF: 0.543 AC: 36873 AN: 67960

Other (OTH) AF: 0.484 AC: 1021 AN: 2110

Alfa AF: 0.520 Hom.: 91009

Bravo AF: 0.462

Asia WGS AF: 0.552 AC: 1920 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.9
DANN	Benign	0.27
PhyloP100		0.089

Splicing

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

Other links and lift over

dbSNP: rs2824292; hg19: chr21-18787176;