rs318173

Positions:

• chrX-97826213-C-A
• chrX-97826213-C-G
• chrX-97826213-C-T

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 0.81 (25668 hom., 26662 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.307

Genes affected

(HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.97826213C>A		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.806 AC: 89006 AN: 110363 Hom.: 25668 Cov.: 23 AF XY: 0.815 AC XY: 26595 AN XY: 32625

Gnomad AFR AF: 0.957

Gnomad AMI AF: 0.904

Gnomad AMR AF: 0.839

Gnomad ASJ AF: 0.785

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.900

Gnomad FIN AF: 0.803

Gnomad MID AF: 0.797

Gnomad NFE AF: 0.696

Gnomad OTH AF: 0.802

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: 0.807 AC: 89067 AN: 110417 Hom.: 25668 Cov.: 23 AF XY: 0.816 AC XY: 26662 AN XY: 32689

Gnomad4 AFR AF: 0.957

Gnomad4 AMR AF: 0.840

Gnomad4 ASJ AF: 0.785

Gnomad4 EAS AF: 0.998

Gnomad4 SAS AF: 0.900

Gnomad4 FIN AF: 0.803

Gnomad4 NFE AF: 0.696

Gnomad4 OTH AF: 0.806

Alfa AF: 0.724 Hom.: 44774

Bravo AF: 0.819

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.5
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs318173; hg19: chrX-97081211;