X-153434261-G-A

Position:

• chrX-153434261-G-A

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 0.59 (14147 hom., 19477 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0700

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.594 AC: 65618 AN: 110461 Hom.: 14147 Cov.: 23 AF XY: 0.595 AC XY: 19462 AN XY: 32721

Gnomad AFR AF: 0.424

Gnomad AMI AF: 0.670

Gnomad AMR AF: 0.616

Gnomad ASJ AF: 0.715

Gnomad EAS AF: 0.651

Gnomad SAS AF: 0.762

Gnomad FIN AF: 0.675

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.660

Gnomad OTH AF: 0.607

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: 0.594 AC: 65624 AN: 110516 Hom.: 14147 Cov.: 23 AF XY: 0.594 AC XY: 19477 AN XY: 32786

Gnomad4 AFR AF: 0.423

Gnomad4 AMR AF: 0.616

Gnomad4 ASJ AF: 0.715

Gnomad4 EAS AF: 0.652

Gnomad4 SAS AF: 0.759

Gnomad4 FIN AF: 0.675

Gnomad4 NFE AF: 0.660

Gnomad4 OTH AF: 0.613

Alfa AF: 0.654 Hom.: 19230

Bravo AF: 0.586

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.91
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs928952; hg19: chrX-152699719;