X-135463627-T-C

Position:

• chrX-135463627-T-C

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 0.56 (12639 hom., 18670 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.799

Genes affected

(HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.135463627T>C		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.565 AC: 62798 AN: 111206 Hom.: 12631 Cov.: 23 AF XY: 0.558 AC XY: 18652 AN XY: 33432

Gnomad AFR AF: 0.558

Gnomad AMI AF: 0.629

Gnomad AMR AF: 0.645

Gnomad ASJ AF: 0.533

Gnomad EAS AF: 0.482

Gnomad SAS AF: 0.386

Gnomad FIN AF: 0.530

Gnomad MID AF: 0.461

Gnomad NFE AF: 0.573

Gnomad OTH AF: 0.533

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: 0.565 AC: 62816 AN: 111261 Hom.: 12639 Cov.: 23 AF XY: 0.557 AC XY: 18670 AN XY: 33497

Gnomad4 AFR AF: 0.557

Gnomad4 AMR AF: 0.644

Gnomad4 ASJ AF: 0.533

Gnomad4 EAS AF: 0.482

Gnomad4 SAS AF: 0.386

Gnomad4 FIN AF: 0.530

Gnomad4 NFE AF: 0.573

Gnomad4 OTH AF: 0.538

Alfa AF: 0.568 Hom.: 4492

Bravo AF: 0.576

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.73
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4320696; hg19: chrX-134597552;