X-147956770-A-G

Position:

• chrX-147956770-A-G

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 0.55 (12686 hom., 17861 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.06

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).

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: 0.549 AC: 60996 AN: 111063 Hom.: 12690 Cov.: 23 AF XY: 0.535 AC XY: 17811 AN XY: 33311

Gnomad AFR AF: 0.743

Gnomad AMI AF: 0.591

Gnomad AMR AF: 0.505

Gnomad ASJ AF: 0.462

Gnomad EAS AF: 0.750

Gnomad SAS AF: 0.465

Gnomad FIN AF: 0.397

Gnomad MID AF: 0.541

Gnomad NFE AF: 0.459

Gnomad OTH AF: 0.563

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: 0.549 AC: 61034 AN: 111117 Hom.: 12686 Cov.: 23 AF XY: 0.535 AC XY: 17861 AN XY: 33375

Gnomad4 AFR AF: 0.743

Gnomad4 AMR AF: 0.505

Gnomad4 ASJ AF: 0.462

Gnomad4 EAS AF: 0.750

Gnomad4 SAS AF: 0.463

Gnomad4 FIN AF: 0.397

Gnomad4 NFE AF: 0.459

Gnomad4 OTH AF: 0.567

Alfa AF: 0.477 Hom.: 20218

Bravo AF: 0.573

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.9
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5904817; hg19: chrX-147038290;