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).

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

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 v4.3

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;