chrX-67808380-C-A

Position:

• chrX-67808380-C-A

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 0.64 (18647 hom., 21855 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.412

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).

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: 0.642 AC: 71246 AN: 110968 Hom.: 18656 Cov.: 23 AF XY: 0.657 AC XY: 21823 AN XY: 33216

Gnomad AFR AF: 0.204

Gnomad AMI AF: 0.874

Gnomad AMR AF: 0.795

Gnomad ASJ AF: 0.802

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.901

Gnomad FIN AF: 0.824

Gnomad MID AF: 0.668

Gnomad NFE AF: 0.797

Gnomad OTH AF: 0.669

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: 0.642 AC: 71257 AN: 111025 Hom.: 18647 Cov.: 23 AF XY: 0.657 AC XY: 21855 AN XY: 33283

Gnomad4 AFR AF: 0.204

Gnomad4 AMR AF: 0.795

Gnomad4 ASJ AF: 0.802

Gnomad4 EAS AF: 0.998

Gnomad4 SAS AF: 0.902

Gnomad4 FIN AF: 0.824

Gnomad4 NFE AF: 0.797

Gnomad4 OTH AF: 0.673

Alfa AF: 0.772 Hom.: 59129

Bravo AF: 0.627

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.4
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4456006; hg19: chrX-67028222;