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).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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

Other links and lift over

dbSNP: rs928952; hg19: chrX-152699719;