X-66054493-C-T

Variant names:

• chrX-66054493-C-T
• rs5918974

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 0.73 (22251 hom., 22943 hem., cov: 21)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00400
• 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=-0.96).

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: 0.726 AC: 79119 AN: 109009 Hom.: 22258 Cov.: 21

Gnomad AFR AF: 0.373

Gnomad AMI AF: 0.872

Gnomad AMR AF: 0.796

Gnomad ASJ AF: 0.813

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.910

Gnomad FIN AF: 0.863

Gnomad MID AF: 0.836

Gnomad NFE AF: 0.864

Gnomad OTH AF: 0.767

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: 0.725 AC: 79124 AN: 109062 Hom.: 22251 Cov.: 21 AF XY: 0.731 AC XY: 22943 AN XY: 31402

African (AFR) AF: 0.373 AC: 11182 AN: 29993

American (AMR) AF: 0.797 AC: 8165 AN: 10250

Ashkenazi Jewish (ASJ) AF: 0.813 AC: 2132 AN: 2623

East Asian (EAS) AF: 0.999 AC: 3436 AN: 3440

South Asian (SAS) AF: 0.909 AC: 2228 AN: 2452

European-Finnish (FIN) AF: 0.863 AC: 4863 AN: 5632

Middle Eastern (MID) AF: 0.824 AC: 173 AN: 210

European-Non Finnish (NFE) AF: 0.865 AC: 45213 AN: 52298

Other (OTH) AF: 0.768 AC: 1148 AN: 1494

Alfa AF: 0.802 Hom.: 114493

Bravo AF: 0.709

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	6.0
DANN	Benign	0.68
PhyloP100		-0.0040

Splicing

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

Other links and lift over

dbSNP: rs5918974; hg19: chrX-65274335;