X-66529354-C-T

Variant names:

• chrX-66529354-C-T
• rs1158928

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 0.71 (20712 hom., 23310 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.30
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).

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: 0.713 AC: 78358 AN: 109892 Hom.: 20715 Cov.: 22

Gnomad AFR AF: 0.442

Gnomad AMI AF: 0.886

Gnomad AMR AF: 0.857

Gnomad ASJ AF: 0.919

Gnomad EAS AF: 0.997

Gnomad SAS AF: 0.902

Gnomad FIN AF: 0.752

Gnomad MID AF: 0.801

Gnomad NFE AF: 0.794

Gnomad OTH AF: 0.753

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: 0.713 AC: 78369 AN: 109943 Hom.: 20712 Cov.: 22 AF XY: 0.722 AC XY: 23310 AN XY: 32271

African (AFR) AF: 0.442 AC: 13399 AN: 30316

American (AMR) AF: 0.858 AC: 8848 AN: 10317

Ashkenazi Jewish (ASJ) AF: 0.919 AC: 2401 AN: 2612

East Asian (EAS) AF: 0.997 AC: 3500 AN: 3511

South Asian (SAS) AF: 0.901 AC: 2315 AN: 2568

European-Finnish (FIN) AF: 0.752 AC: 4313 AN: 5739

Middle Eastern (MID) AF: 0.805 AC: 169 AN: 210

European-Non Finnish (NFE) AF: 0.794 AC: 41689 AN: 52492

Other (OTH) AF: 0.756 AC: 1137 AN: 1503

Alfa AF: 0.659 Hom.: 9207

Bravo AF: 0.711

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.27
PhyloP100		-1.3

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: rs1158928;

hg19: chrX-65749196;