X-145231305-A-G

Position:

• chrX-145231305-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 0.54 (11747 hom., 17782 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.885

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.540 AC: 59693 AN: 110506 Hom.: 11751 Cov.: 23 AF XY: 0.541 AC XY: 17735 AN XY: 32762

Gnomad AFR AF: 0.602

Gnomad AMI AF: 0.402

Gnomad AMR AF: 0.667

Gnomad ASJ AF: 0.394

Gnomad EAS AF: 0.847

Gnomad SAS AF: 0.631

Gnomad FIN AF: 0.535

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.466

Gnomad OTH AF: 0.522

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: 0.540 AC: 59737 AN: 110558 Hom.: 11747 Cov.: 23 AF XY: 0.542 AC XY: 17782 AN XY: 32824

Gnomad4 AFR AF: 0.603

Gnomad4 AMR AF: 0.667

Gnomad4 ASJ AF: 0.394

Gnomad4 EAS AF: 0.846

Gnomad4 SAS AF: 0.628

Gnomad4 FIN AF: 0.535

Gnomad4 NFE AF: 0.466

Gnomad4 OTH AF: 0.523

Alfa AF: 0.463 Hom.: 15337

Bravo AF: 0.559

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.0
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5920468; hg19: chrX-144312825;