X-67801708-C-T

Position:

• chrX-67801708-C-T

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 0.69 (19902 hom., 22728 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.111

Genes affected

(HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.67801708C>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.693 AC: 76210 AN: 109912 Hom.: 19907 Cov.: 22 AF XY: 0.705 AC XY: 22690 AN XY: 32188

Gnomad AFR AF: 0.380

Gnomad AMI AF: 0.873

Gnomad AMR AF: 0.815

Gnomad ASJ AF: 0.801

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.904

Gnomad FIN AF: 0.822

Gnomad MID AF: 0.674

Gnomad NFE AF: 0.797

Gnomad OTH AF: 0.709

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: 0.693 AC: 76234 AN: 109964 Hom.: 19902 Cov.: 22 AF XY: 0.705 AC XY: 22728 AN XY: 32250

Gnomad4 AFR AF: 0.380

Gnomad4 AMR AF: 0.815

Gnomad4 ASJ AF: 0.801

Gnomad4 EAS AF: 0.998

Gnomad4 SAS AF: 0.905

Gnomad4 FIN AF: 0.822

Gnomad4 NFE AF: 0.797

Gnomad4 OTH AF: 0.713

Alfa AF: 0.785 Hom.: 71000

Bravo AF: 0.685

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.3
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5919432; hg19: chrX-67021550;