X-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).

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: 0.669 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 v4.3

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

Other links and lift over

dbSNP: rs4131729; hg19: chrX-51697194;