21-24119738-A-G

Variant names:

• chr21-24119738-A-G
• rs1699672

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 0.371 in 151,782 control chromosomes in the GnomAD database, including 11,462 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 0.37 (11462 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0390
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.525 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.371 AC: 56215 AN: 151664 Hom.: 11438 Cov.: 32

Gnomad AFR AF: 0.531

Gnomad AMI AF: 0.455

Gnomad AMR AF: 0.404

Gnomad ASJ AF: 0.293

Gnomad EAS AF: 0.409

Gnomad SAS AF: 0.343

Gnomad FIN AF: 0.261

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.287

Gnomad OTH AF: 0.322

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

GnomAD4 genome AF: 0.371 AC: 56301 AN: 151782 Hom.: 11462 Cov.: 32 AF XY: 0.371 AC XY: 27512 AN XY: 74136

African (AFR) AF: 0.531 AC: 21966 AN: 41360

American (AMR) AF: 0.404 AC: 6163 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.293 AC: 1016 AN: 3468

East Asian (EAS) AF: 0.410 AC: 2115 AN: 5154

South Asian (SAS) AF: 0.345 AC: 1659 AN: 4808

European-Finnish (FIN) AF: 0.261 AC: 2745 AN: 10512

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.287 AC: 19476 AN: 67914

Other (OTH) AF: 0.326 AC: 689 AN: 2112

Alfa AF: 0.319 Hom.: 1065

Bravo AF: 0.387

Asia WGS AF: 0.395 AC: 1368 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.9
DANN	Benign	0.52
PhyloP100		0.039

Splicing

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

Other links and lift over

dbSNP: rs1699672; hg19: chr21-25492051;