X-117075605-C-T

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_Strong BS2

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 0.88 (30578 hom., 28929 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BS2: High Homozygotes in GnomAd at 30583 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.877 AC: 97049 AN: 110656 Hom.: 30583 Cov.: 23 AF XY: 0.879 AC XY: 28888 AN XY: 32852

Gnomad AFR AF: 0.681

Gnomad AMI AF: 0.999

Gnomad AMR AF: 0.854

Gnomad ASJ AF: 0.980

Gnomad EAS AF: 0.765

Gnomad SAS AF: 0.871

Gnomad FIN AF: 0.992

Gnomad MID AF: 0.910

Gnomad NFE AF: 0.982

Gnomad OTH AF: 0.877

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: 0.877 AC: 97078 AN: 110713 Hom.: 30578 Cov.: 23 AF XY: 0.879 AC XY: 28929 AN XY: 32917

Gnomad4 AFR AF: 0.681

Gnomad4 AMR AF: 0.852

Gnomad4 ASJ AF: 0.980

Gnomad4 EAS AF: 0.765

Gnomad4 SAS AF: 0.872

Gnomad4 FIN AF: 0.992

Gnomad4 NFE AF: 0.982

Gnomad4 OTH AF: 0.878

Alfa AF: 0.910 Hom.: 16872

Bravo AF: 0.853

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.0
Dann	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5909759; hg19: chrX-116209573;