rs1381733

Positions:

• chrX-100014722-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 0.64 (16749 hom., 21060 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.446

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).

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: 0.638 AC: 70346 AN: 110211 Hom.: 16750 Cov.: 23 AF XY: 0.647 AC XY: 21032 AN XY: 32513

Gnomad AFR AF: 0.382

Gnomad AMI AF: 0.897

Gnomad AMR AF: 0.724

Gnomad ASJ AF: 0.623

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.888

Gnomad FIN AF: 0.746

Gnomad MID AF: 0.530

Gnomad NFE AF: 0.718

Gnomad OTH AF: 0.656

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: 0.638 AC: 70368 AN: 110264 Hom.: 16749 Cov.: 23 AF XY: 0.646 AC XY: 21060 AN XY: 32576

Gnomad4 AFR AF: 0.382

Gnomad4 AMR AF: 0.724

Gnomad4 ASJ AF: 0.623

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.888

Gnomad4 FIN AF: 0.746

Gnomad4 NFE AF: 0.718

Gnomad4 OTH AF: 0.661

Alfa AF: 0.710 Hom.: 19774

Bravo AF: 0.630

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.15
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1381733; hg19: chrX-99269720;