chrX-55366646-T-C

Variant names:

• chrX-55366646-T-C
• rs4240023

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 0.85 (29381 hom., 28355 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.82
• 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=-1.07).

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: 0.851 AC: 94266 AN: 110826 Hom.: 29390 Cov.: 23

Gnomad AFR AF: 0.543

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.926

Gnomad ASJ AF: 0.945

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.944

Gnomad FIN AF: 0.994

Gnomad MID AF: 0.825

Gnomad NFE AF: 0.975

Gnomad OTH AF: 0.863

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: 0.851 AC: 94304 AN: 110875 Hom.: 29381 Cov.: 23 AF XY: 0.857 AC XY: 28355 AN XY: 33099

African (AFR) AF: 0.544 AC: 16539 AN: 30427

American (AMR) AF: 0.926 AC: 9576 AN: 10343

Ashkenazi Jewish (ASJ) AF: 0.945 AC: 2500 AN: 2645

East Asian (EAS) AF: 1.00 AC: 3547 AN: 3547

South Asian (SAS) AF: 0.944 AC: 2441 AN: 2587

European-Finnish (FIN) AF: 0.994 AC: 5795 AN: 5828

Middle Eastern (MID) AF: 0.831 AC: 182 AN: 219

European-Non Finnish (NFE) AF: 0.975 AC: 51737 AN: 53089

Other (OTH) AF: 0.865 AC: 1303 AN: 1506

Alfa AF: 0.827 Hom.: 4645

Bravo AF: 0.834

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.21
DANN	Benign	0.43
PhyloP100		-3.8

Splicing

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

Other links and lift over

dbSNP: rs4240023; hg19: chrX-55393079;