chrX-116528159-C-G

Variant names:

• chrX-116528159-C-G
• rs988457

Variant summary

Our verdict is Likely benign. The variant received -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
• Publications: 2 publications found

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.492 AC: 53760 AN: 109275 Hom.: 9639 Cov.: 22

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

African (AFR) AF: 0.460 AC: 13872 AN: 30161

American (AMR) AF: 0.454 AC: 4634 AN: 10217

Ashkenazi Jewish (ASJ) AF: 0.497 AC: 1300 AN: 2617

East Asian (EAS) AF: 0.314 AC: 1072 AN: 3413

South Asian (SAS) AF: 0.504 AC: 1283 AN: 2545

European-Finnish (FIN) AF: 0.487 AC: 2748 AN: 5638

Middle Eastern (MID) AF: 0.471 AC: 98 AN: 208

European-Non Finnish (NFE) AF: 0.530 AC: 27759 AN: 52390

Other (OTH) AF: 0.502 AC: 739 AN: 1472

Alfa AF: 0.517 Hom.: 3741

Bravo AF: 0.489

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.9
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs988457; hg19: chrX-115659328;