X-133526341-G-A

Variant names:

• chrX-133526341-G-A
• rs2188457

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 0.279 in 110,688 control chromosomes in the GnomAD database, including 5,418 homozygotes. There are 8,774 hemizygotes in GnomAD. 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 0.28 (5418 hom., 8774 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.484
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.622 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.279 AC: 30823 AN: 110635 Hom.: 5406 Cov.: 23

Gnomad AFR AF: 0.630

Gnomad AMI AF: 0.170

Gnomad AMR AF: 0.172

Gnomad ASJ AF: 0.151

Gnomad EAS AF: 0.520

Gnomad SAS AF: 0.451

Gnomad FIN AF: 0.0837

Gnomad MID AF: 0.200

Gnomad NFE AF: 0.106

Gnomad OTH AF: 0.258

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

GnomAD4 genome AF: 0.279 AC: 30873 AN: 110688 Hom.: 5418 Cov.: 23 AF XY: 0.266 AC XY: 8774 AN XY: 32988

African (AFR) AF: 0.630 AC: 19058 AN: 30255

American (AMR) AF: 0.172 AC: 1797 AN: 10442

Ashkenazi Jewish (ASJ) AF: 0.151 AC: 397 AN: 2635

East Asian (EAS) AF: 0.519 AC: 1793 AN: 3453

South Asian (SAS) AF: 0.451 AC: 1145 AN: 2537

European-Finnish (FIN) AF: 0.0837 AC: 507 AN: 6055

Middle Eastern (MID) AF: 0.201 AC: 43 AN: 214

European-Non Finnish (NFE) AF: 0.106 AC: 5619 AN: 52907

Other (OTH) AF: 0.263 AC: 400 AN: 1519

Alfa AF: 0.184 Hom.: 18390

Bravo AF: 0.302

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.2
DANN	Benign	0.50
PhyloP100		0.48

Splicing

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

Other links and lift over

dbSNP: rs2188457; hg19: chrX-132660369;