X-101690351-G-C

Position:

• chrX-101690351-G-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 (24039 hom., 25442 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.117

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.780 AC: 86257 AN: 110525 Hom.: 24041 Cov.: 23 AF XY: 0.776 AC XY: 25386 AN XY: 32727

Gnomad AFR AF: 0.868

Gnomad AMI AF: 0.937

Gnomad AMR AF: 0.844

Gnomad ASJ AF: 0.734

Gnomad EAS AF: 0.837

Gnomad SAS AF: 0.840

Gnomad FIN AF: 0.613

Gnomad MID AF: 0.739

Gnomad NFE AF: 0.730

Gnomad OTH AF: 0.770

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: 0.780 AC: 86306 AN: 110580 Hom.: 24039 Cov.: 23 AF XY: 0.776 AC XY: 25442 AN XY: 32792

Gnomad4 AFR AF: 0.868

Gnomad4 AMR AF: 0.844

Gnomad4 ASJ AF: 0.734

Gnomad4 EAS AF: 0.838

Gnomad4 SAS AF: 0.840

Gnomad4 FIN AF: 0.613

Gnomad4 NFE AF: 0.730

Gnomad4 OTH AF: 0.771

Alfa AF: 0.611 Hom.: 2537

Bravo AF: 0.801

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6621148; hg19: chrX-100945351;