X-44055387-T-C

Position:

• chrX-44055387-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 0.78 (23928 hom., 25659 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.65

Genes affected

(HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.65).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.44055387T>C		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.782 AC: 86489 AN: 110613 Hom.: 23938 Cov.: 23 AF XY: 0.780 AC XY: 25596 AN XY: 32805

Gnomad AFR AF: 0.860

Gnomad AMI AF: 0.647

Gnomad AMR AF: 0.785

Gnomad ASJ AF: 0.752

Gnomad EAS AF: 0.895

Gnomad SAS AF: 0.809

Gnomad FIN AF: 0.720

Gnomad MID AF: 0.689

Gnomad NFE AF: 0.738

Gnomad OTH AF: 0.788

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: 0.782 AC: 86537 AN: 110671 Hom.: 23928 Cov.: 23 AF XY: 0.781 AC XY: 25659 AN XY: 32871

Gnomad4 AFR AF: 0.860

Gnomad4 AMR AF: 0.785

Gnomad4 ASJ AF: 0.752

Gnomad4 EAS AF: 0.895

Gnomad4 SAS AF: 0.809

Gnomad4 FIN AF: 0.720

Gnomad4 NFE AF: 0.738

Gnomad4 OTH AF: 0.785

Alfa AF: 0.751 Hom.: 55491

Bravo AF: 0.793

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	4.2
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1375329; hg19: chrX-43914633;