rs1293470

chrX-123078079-A-G

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_Strong BS2

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 0.69 (19054 hom., 22372 hem., cov: 24)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.16

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BS2: High Homozygotes in GnomAd at 19056 gene

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: 0.686 AC: 76023 AN: 110895 Hom.: 19056 Cov.: 24 AF XY: 0.673 AC XY: 22332 AN XY: 33179

Gnomad AFR AF: 0.733

Gnomad AMI AF: 0.810

Gnomad AMR AF: 0.535

Gnomad ASJ AF: 0.791

Gnomad EAS AF: 0.228

Gnomad SAS AF: 0.392

Gnomad FIN AF: 0.678

Gnomad MID AF: 0.734

Gnomad NFE AF: 0.726

Gnomad OTH AF: 0.702

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: 0.686 AC: 76058 AN: 110948 Hom.: 19054 Cov.: 24 AF XY: 0.673 AC XY: 22372 AN XY: 33242

Gnomad4 AFR AF: 0.733

Gnomad4 AMR AF: 0.534

Gnomad4 ASJ AF: 0.791

Gnomad4 EAS AF: 0.228

Gnomad4 SAS AF: 0.390

Gnomad4 FIN AF: 0.678

Gnomad4 NFE AF: 0.726

Gnomad4 OTH AF: 0.702

Alfa AF: 0.692 Hom.: 19568

Bravo AF: 0.673

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	7.0
Dann	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1293470; hg19: chrX-122211932;