chrX-51954098-C-T

Variant names:

• chrX-51954098-C-T
• rs4131729

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 0.67 (17599 hom., 21914 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.110
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).

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: 0.669 AC: 73821 AN: 110287 Hom.: 17595 Cov.: 23

Gnomad AFR AF: 0.569

Gnomad AMI AF: 0.782

Gnomad AMR AF: 0.798

Gnomad ASJ AF: 0.755

Gnomad EAS AF: 0.867

Gnomad SAS AF: 0.768

Gnomad FIN AF: 0.625

Gnomad MID AF: 0.671

Gnomad NFE AF: 0.682

Gnomad OTH AF: 0.696

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: 0.669 AC: 73837 AN: 110336 Hom.: 17599 Cov.: 23 AF XY: 0.672 AC XY: 21914 AN XY: 32602

African (AFR) AF: 0.568 AC: 17251 AN: 30353

American (AMR) AF: 0.798 AC: 8225 AN: 10304

Ashkenazi Jewish (ASJ) AF: 0.755 AC: 1981 AN: 2623

East Asian (EAS) AF: 0.868 AC: 3039 AN: 3502

South Asian (SAS) AF: 0.766 AC: 1980 AN: 2586

European-Finnish (FIN) AF: 0.625 AC: 3618 AN: 5793

Middle Eastern (MID) AF: 0.657 AC: 142 AN: 216

European-Non Finnish (NFE) AF: 0.682 AC: 36011 AN: 52765

Other (OTH) AF: 0.699 AC: 1063 AN: 1520

Alfa AF: 0.689 Hom.: 42510

Bravo AF: 0.681

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.2
DANN	Benign	0.56
PhyloP100		-0.11

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: rs4131729;

hg19: chrX-51697194;