X-141278334-A-G

Position:

• chrX-141278334-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 0.64 (16779 hom., 20770 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.951

Genes affected

(HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.141278334A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SPANXA2-OT1	ENST00000662492.1	n.102+90497A>G		intron_variant

Frequencies

GnomAD3 genomes AF: 0.643 AC: 70931 AN: 110258 Hom.: 16785 Cov.: 23 AF XY: 0.638 AC XY: 20725 AN XY: 32506

Gnomad AFR AF: 0.471

Gnomad AMI AF: 0.559

Gnomad AMR AF: 0.626

Gnomad ASJ AF: 0.704

Gnomad EAS AF: 0.573

Gnomad SAS AF: 0.644

Gnomad FIN AF: 0.674

Gnomad MID AF: 0.734

Gnomad NFE AF: 0.744

Gnomad OTH AF: 0.672

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: 0.643 AC: 70970 AN: 110313 Hom.: 16779 Cov.: 23 AF XY: 0.638 AC XY: 20770 AN XY: 32571

Gnomad4 AFR AF: 0.471

Gnomad4 AMR AF: 0.627

Gnomad4 ASJ AF: 0.704

Gnomad4 EAS AF: 0.573

Gnomad4 SAS AF: 0.647

Gnomad4 FIN AF: 0.674

Gnomad4 NFE AF: 0.744

Gnomad4 OTH AF: 0.673

Alfa AF: 0.714 Hom.: 26313

Bravo AF: 0.631

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	7.2

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs845165; hg19: chrX-140372474;