X-15189904-C-T

Position:

• chrX-15189904-C-T

Variant summary

Our verdict is Likely benign. Variant got -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 0.55 (11895 hom., 17878 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.605

Genes affected

(HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.15189904C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.548 AC: 60406 AN: 110205 Hom.: 11897 Cov.: 23 AF XY: 0.549 AC XY: 17843 AN XY: 32513

Gnomad AFR AF: 0.569

Gnomad AMI AF: 0.222

Gnomad AMR AF: 0.630

Gnomad ASJ AF: 0.599

Gnomad EAS AF: 0.862

Gnomad SAS AF: 0.570

Gnomad FIN AF: 0.464

Gnomad MID AF: 0.526

Gnomad NFE AF: 0.508

Gnomad OTH AF: 0.565

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: 0.548 AC: 60436 AN: 110255 Hom.: 11895 Cov.: 23 AF XY: 0.549 AC XY: 17878 AN XY: 32573

Gnomad4 AFR AF: 0.569

Gnomad4 AMR AF: 0.630

Gnomad4 ASJ AF: 0.599

Gnomad4 EAS AF: 0.862

Gnomad4 SAS AF: 0.567

Gnomad4 FIN AF: 0.464

Gnomad4 NFE AF: 0.508

Gnomad4 OTH AF: 0.570

Alfa AF: 0.516 Hom.: 3728

Bravo AF: 0.565

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.12
DANN	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1993969; hg19: chrX-15208026;