X-93668425-C-T

Variant names:

• chrX-93668425-C-T
• rs5983240

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 0.54 (12011 hom., 17602 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.35
• Publications: 0 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: 0.544 AC: 60088 AN: 110364 Hom.: 12004 Cov.: 22

Gnomad AFR AF: 0.703

Gnomad AMI AF: 0.328

Gnomad AMR AF: 0.502

Gnomad ASJ AF: 0.518

Gnomad EAS AF: 0.468

Gnomad SAS AF: 0.570

Gnomad FIN AF: 0.518

Gnomad MID AF: 0.511

Gnomad NFE AF: 0.473

Gnomad OTH AF: 0.526

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: 0.545 AC: 60155 AN: 110418 Hom.: 12011 Cov.: 22 AF XY: 0.539 AC XY: 17602 AN XY: 32654

African (AFR) AF: 0.704 AC: 21346 AN: 30342

American (AMR) AF: 0.502 AC: 5214 AN: 10390

Ashkenazi Jewish (ASJ) AF: 0.518 AC: 1360 AN: 2625

East Asian (EAS) AF: 0.468 AC: 1627 AN: 3475

South Asian (SAS) AF: 0.573 AC: 1492 AN: 2603

European-Finnish (FIN) AF: 0.518 AC: 3018 AN: 5824

Middle Eastern (MID) AF: 0.519 AC: 110 AN: 212

European-Non Finnish (NFE) AF: 0.473 AC: 24980 AN: 52771

Other (OTH) AF: 0.524 AC: 787 AN: 1502

Alfa AF: 0.498 Hom.: 62412

Bravo AF: 0.551

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.056
DANN	Benign	0.42
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs5983240; hg19: chrX-92923424;