X-78327951-C-T

Position:

• chrX-78327951-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 0.79 (24654 hom., 25779 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0220

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).

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: 0.787 AC: 87218 AN: 110841 Hom.: 24660 Cov.: 23 AF XY: 0.778 AC XY: 25724 AN XY: 33053

Gnomad AFR AF: 0.904

Gnomad AMI AF: 0.663

Gnomad AMR AF: 0.672

Gnomad ASJ AF: 0.815

Gnomad EAS AF: 0.595

Gnomad SAS AF: 0.623

Gnomad FIN AF: 0.777

Gnomad MID AF: 0.744

Gnomad NFE AF: 0.765

Gnomad OTH AF: 0.757

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: 0.787 AC: 87261 AN: 110899 Hom.: 24654 Cov.: 23 AF XY: 0.778 AC XY: 25779 AN XY: 33121

Gnomad4 AFR AF: 0.904

Gnomad4 AMR AF: 0.671

Gnomad4 ASJ AF: 0.815

Gnomad4 EAS AF: 0.594

Gnomad4 SAS AF: 0.621

Gnomad4 FIN AF: 0.777

Gnomad4 NFE AF: 0.765

Gnomad4 OTH AF: 0.753

Alfa AF: 0.773 Hom.: 11582

Bravo AF: 0.784

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.49
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2806489; hg19: chrX-77583448;