rs5980075

Positions:

• chrX-14932409-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 0.63 (15959 hom., 19763 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0700

Genes affected

(HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.14932409A>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.626 AC: 68883 AN: 110004 Hom.: 15967 Cov.: 22 AF XY: 0.611 AC XY: 19718 AN XY: 32280

Gnomad AFR AF: 0.733

Gnomad AMI AF: 0.879

Gnomad AMR AF: 0.531

Gnomad ASJ AF: 0.559

Gnomad EAS AF: 0.185

Gnomad SAS AF: 0.411

Gnomad FIN AF: 0.626

Gnomad MID AF: 0.586

Gnomad NFE AF: 0.625

Gnomad OTH AF: 0.593

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: 0.626 AC: 68910 AN: 110056 Hom.: 15959 Cov.: 22 AF XY: 0.611 AC XY: 19763 AN XY: 32342

Gnomad4 AFR AF: 0.733

Gnomad4 AMR AF: 0.530

Gnomad4 ASJ AF: 0.559

Gnomad4 EAS AF: 0.185

Gnomad4 SAS AF: 0.410

Gnomad4 FIN AF: 0.626

Gnomad4 NFE AF: 0.625

Gnomad4 OTH AF: 0.589

Alfa AF: 0.615 Hom.: 15748

Bravo AF: 0.623

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.8
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5980075; hg19: chrX-14950531;