X-67140772-T-C

Position:

• chrX-67140772-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 0.66 (20423 hom., 21605 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.397

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).

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: 0.657 AC: 72283 AN: 109971 Hom.: 20430 Cov.: 22 AF XY: 0.667 AC XY: 21590 AN XY: 32351

Gnomad AFR AF: 0.155

Gnomad AMI AF: 0.887

Gnomad AMR AF: 0.829

Gnomad ASJ AF: 0.920

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.917

Gnomad FIN AF: 0.828

Gnomad MID AF: 0.763

Gnomad NFE AF: 0.843

Gnomad OTH AF: 0.702

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: 0.657 AC: 72278 AN: 110025 Hom.: 20423 Cov.: 22 AF XY: 0.667 AC XY: 21605 AN XY: 32415

Gnomad4 AFR AF: 0.155

Gnomad4 AMR AF: 0.829

Gnomad4 ASJ AF: 0.920

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.917

Gnomad4 FIN AF: 0.828

Gnomad4 NFE AF: 0.843

Gnomad4 OTH AF: 0.704

Alfa AF: 0.756 Hom.: 11533

Bravo AF: 0.641

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.2
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5919287; hg19: chrX-66360614;