chr21-17409363-G-A

Variant names:

• chr21-17409363-G-A
• rs8127220

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 0.129 in 152,114 control chromosomes in the GnomAD database, including 2,347 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 0.13 (2347 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0690
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.318 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: 0.129 AC: 19549 AN: 151996 Hom.: 2334 Cov.: 32

Gnomad AFR AF: 0.322

Gnomad AMI AF: 0.0219

Gnomad AMR AF: 0.0692

Gnomad ASJ AF: 0.0282

Gnomad EAS AF: 0.0488

Gnomad SAS AF: 0.0147

Gnomad FIN AF: 0.0513

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0587

Gnomad OTH AF: 0.102

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

GnomAD4 genome AF: 0.129 AC: 19606 AN: 152114 Hom.: 2347 Cov.: 32 AF XY: 0.125 AC XY: 9262 AN XY: 74386

African (AFR) AF: 0.322 AC: 13344 AN: 41418

American (AMR) AF: 0.0691 AC: 1056 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.0282 AC: 98 AN: 3470

East Asian (EAS) AF: 0.0491 AC: 254 AN: 5176

South Asian (SAS) AF: 0.0145 AC: 70 AN: 4828

European-Finnish (FIN) AF: 0.0513 AC: 544 AN: 10612

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0587 AC: 3993 AN: 68014

Other (OTH) AF: 0.101 AC: 213 AN: 2116

Alfa AF: 0.0848 Hom.: 2836

Bravo AF: 0.142

Asia WGS AF: 0.0400 AC: 138 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.9
DANN	Benign	0.57
PhyloP100		0.069

Splicing

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

Other links and lift over

dbSNP: rs8127220; hg19: chr21-18781682;