rs928952

Variant names:

• chrX-153434261-G-A
• rs928952

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

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 0.59 (14147 hom., 19477 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0700
• Publications: 4 publications found

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).

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: 0.594 AC: 65618 AN: 110461 Hom.: 14147 Cov.: 23

Gnomad AFR AF: 0.424

Gnomad AMI AF: 0.670

Gnomad AMR AF: 0.616

Gnomad ASJ AF: 0.715

Gnomad EAS AF: 0.651

Gnomad SAS AF: 0.762

Gnomad FIN AF: 0.675

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.660

Gnomad OTH AF: 0.607

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

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.594 AC: 65624 AN: 110516 Hom.: 14147 Cov.: 23 AF XY: 0.594 AC XY: 19477 AN XY: 32786

African (AFR) AF: 0.423 AC: 12883 AN: 30458

American (AMR) AF: 0.616 AC: 6434 AN: 10449

Ashkenazi Jewish (ASJ) AF: 0.715 AC: 1880 AN: 2630

East Asian (EAS) AF: 0.652 AC: 2264 AN: 3471

South Asian (SAS) AF: 0.759 AC: 1946 AN: 2563

European-Finnish (FIN) AF: 0.675 AC: 3903 AN: 5785

Middle Eastern (MID) AF: 0.628 AC: 135 AN: 215

European-Non Finnish (NFE) AF: 0.660 AC: 34804 AN: 52766

Other (OTH) AF: 0.613 AC: 922 AN: 1503

Alfa AF: 0.646 Hom.: 31920

Bravo AF: 0.586

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.91
DANN	Benign	0.44
PhyloP100		-0.070

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs928952;

hg19: chrX-152699719;