X-5266661-C-T

Position:

• chrX-5266661-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 0.56 (13068 hom., 18321 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.358

Genes affected

(HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.5266661C>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.564 AC: 62363 AN: 110630 Hom.: 13062 Cov.: 23 AF XY: 0.556 AC XY: 18287 AN XY: 32918

Gnomad AFR AF: 0.738

Gnomad AMI AF: 0.544

Gnomad AMR AF: 0.502

Gnomad ASJ AF: 0.533

Gnomad EAS AF: 0.630

Gnomad SAS AF: 0.382

Gnomad FIN AF: 0.452

Gnomad MID AF: 0.600

Gnomad NFE AF: 0.495

Gnomad OTH AF: 0.544

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: 0.564 AC: 62406 AN: 110679 Hom.: 13068 Cov.: 23 AF XY: 0.556 AC XY: 18321 AN XY: 32977

Gnomad4 AFR AF: 0.738

Gnomad4 AMR AF: 0.502

Gnomad4 ASJ AF: 0.533

Gnomad4 EAS AF: 0.630

Gnomad4 SAS AF: 0.383

Gnomad4 FIN AF: 0.452

Gnomad4 NFE AF: 0.495

Gnomad4 OTH AF: 0.544

Alfa AF: 0.532 Hom.: 7130

Bravo AF: 0.578

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.17
DANN	Benign	0.21

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6638512; hg19: chrX-5184702; COSMIC: COSV56546748;