X-116528159-C-G

Variant names:

• chrX-116528159-C-G
• rs988457

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 0.49 (9633 hom., 15353 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.200

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.492 AC: 53760 AN: 109275 Hom.: 9639 Cov.: 22 AF XY: 0.484 AC XY: 15323 AN XY: 31655

Gnomad AFR AF: 0.460

Gnomad AMI AF: 0.410

Gnomad AMR AF: 0.454

Gnomad ASJ AF: 0.497

Gnomad EAS AF: 0.314

Gnomad SAS AF: 0.505

Gnomad FIN AF: 0.487

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.530

Gnomad OTH AF: 0.503

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: 0.492 AC: 53777 AN: 109325 Hom.: 9633 Cov.: 22 AF XY: 0.484 AC XY: 15353 AN XY: 31715

Gnomad4 AFR AF: 0.460

Gnomad4 AMR AF: 0.454

Gnomad4 ASJ AF: 0.497

Gnomad4 EAS AF: 0.314

Gnomad4 SAS AF: 0.504

Gnomad4 FIN AF: 0.487

Gnomad4 NFE AF: 0.530

Gnomad4 OTH AF: 0.502

Alfa AF: 0.517 Hom.: 3741

Bravo AF: 0.489

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.9

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs988457; hg19: chrX-115659328;