22-21625000-T-C

Variant names:

• chr22-21625000-T-C
• rs4821124

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 0.193 in 152,190 control chromosomes in the GnomAD database, including 3,528 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 0.19 (3528 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.74
• Publications: 51 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.393 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: 0.193 AC: 29289 AN: 152072 Hom.: 3520 Cov.: 32

Gnomad AFR AF: 0.0804

Gnomad AMI AF: 0.129

Gnomad AMR AF: 0.307

Gnomad ASJ AF: 0.235

Gnomad EAS AF: 0.406

Gnomad SAS AF: 0.269

Gnomad FIN AF: 0.322

Gnomad MID AF: 0.248

Gnomad NFE AF: 0.192

Gnomad OTH AF: 0.201

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

GnomAD4 genome AF: 0.193 AC: 29308 AN: 152190 Hom.: 3528 Cov.: 32 AF XY: 0.204 AC XY: 15143 AN XY: 74394

African (AFR) AF: 0.0806 AC: 3349 AN: 41538

American (AMR) AF: 0.308 AC: 4709 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.235 AC: 817 AN: 3472

East Asian (EAS) AF: 0.407 AC: 2102 AN: 5164

South Asian (SAS) AF: 0.267 AC: 1288 AN: 4826

European-Finnish (FIN) AF: 0.322 AC: 3404 AN: 10586

Middle Eastern (MID) AF: 0.229 AC: 67 AN: 292

European-Non Finnish (NFE) AF: 0.192 AC: 13029 AN: 68010

Other (OTH) AF: 0.201 AC: 425 AN: 2114

Alfa AF: 0.192 Hom.: 1833

Bravo AF: 0.192

Asia WGS AF: 0.320 AC: 1114 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.14
DANN	Benign	0.69
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs4821124; hg19: chr22-21979289;