X-114556657-T-C

Position:

• chrX-114556657-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 0.81 (25774 hom., 26721 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.163

Genes affected

(HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.114556657T>C		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.815 AC: 89889 AN: 110298 Hom.: 25784 Cov.: 23 AF XY: 0.820 AC XY: 26688 AN XY: 32530

Gnomad AFR AF: 0.778

Gnomad AMI AF: 0.818

Gnomad AMR AF: 0.808

Gnomad ASJ AF: 0.779

Gnomad EAS AF: 0.975

Gnomad SAS AF: 0.890

Gnomad FIN AF: 0.864

Gnomad MID AF: 0.760

Gnomad NFE AF: 0.819

Gnomad OTH AF: 0.834

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: 0.815 AC: 89907 AN: 110348 Hom.: 25774 Cov.: 23 AF XY: 0.820 AC XY: 26721 AN XY: 32590

Gnomad4 AFR AF: 0.778

Gnomad4 AMR AF: 0.807

Gnomad4 ASJ AF: 0.779

Gnomad4 EAS AF: 0.975

Gnomad4 SAS AF: 0.891

Gnomad4 FIN AF: 0.864

Gnomad4 NFE AF: 0.819

Gnomad4 OTH AF: 0.836

Alfa AF: 0.721 Hom.: 3196

Bravo AF: 0.806

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	4.7

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs519161; hg19: chrX-113791114;