X-152487090-T-C

Position:

• chrX-152487090-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 0.63 (16982 hom., 20349 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.109

Genes affected

(HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.152487090T>C		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.626 AC: 69066 AN: 110244 Hom.: 16993 Cov.: 23 AF XY: 0.625 AC XY: 20326 AN XY: 32520

Gnomad AFR AF: 0.329

Gnomad AMI AF: 0.956

Gnomad AMR AF: 0.565

Gnomad ASJ AF: 0.677

Gnomad EAS AF: 0.416

Gnomad SAS AF: 0.615

Gnomad FIN AF: 0.851

Gnomad MID AF: 0.734

Gnomad NFE AF: 0.793

Gnomad OTH AF: 0.638

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: 0.626 AC: 69056 AN: 110293 Hom.: 16982 Cov.: 23 AF XY: 0.625 AC XY: 20349 AN XY: 32579

Gnomad4 AFR AF: 0.328

Gnomad4 AMR AF: 0.565

Gnomad4 ASJ AF: 0.677

Gnomad4 EAS AF: 0.416

Gnomad4 SAS AF: 0.616

Gnomad4 FIN AF: 0.851

Gnomad4 NFE AF: 0.793

Gnomad4 OTH AF: 0.629

Alfa AF: 0.716 Hom.: 19069

Bravo AF: 0.594

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.7
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10856240; hg19: chrX-151655562;