22-25411037-T-G

Variant names:

• chr22-25411037-T-G
• rs133252

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 0.833 in 151,898 control chromosomes in the GnomAD database, including 52,853 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 0.83 (52853 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.02
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.875 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: 0.833 AC: 126465 AN: 151780 Hom.: 52802 Cov.: 34

Gnomad AFR AF: 0.874

Gnomad AMI AF: 0.715

Gnomad AMR AF: 0.832

Gnomad ASJ AF: 0.821

Gnomad EAS AF: 0.896

Gnomad SAS AF: 0.882

Gnomad FIN AF: 0.805

Gnomad MID AF: 0.791

Gnomad NFE AF: 0.808

Gnomad OTH AF: 0.829

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

GnomAD4 genome AF: 0.833 AC: 126576 AN: 151898 Hom.: 52853 Cov.: 34 AF XY: 0.833 AC XY: 61866 AN XY: 74226

African (AFR) AF: 0.874 AC: 36168 AN: 41392

American (AMR) AF: 0.832 AC: 12690 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.821 AC: 2848 AN: 3470

East Asian (EAS) AF: 0.896 AC: 4632 AN: 5168

South Asian (SAS) AF: 0.883 AC: 4245 AN: 4810

European-Finnish (FIN) AF: 0.805 AC: 8499 AN: 10564

Middle Eastern (MID) AF: 0.789 AC: 232 AN: 294

European-Non Finnish (NFE) AF: 0.808 AC: 54864 AN: 67922

Other (OTH) AF: 0.829 AC: 1746 AN: 2106

Alfa AF: 0.817 Hom.: 7416

Bravo AF: 0.834

Asia WGS AF: 0.886 AC: 3084 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.77
DANN	Benign	0.55
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs133252; hg19: chr22-25807004;