X-67808380-C-A

Variant names:

• chrX-67808380-C-A
• rs4456006

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 0.64 (18647 hom., 21855 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.412
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).

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: 0.642 AC: 71246 AN: 110968 Hom.: 18656 Cov.: 23

Gnomad AFR AF: 0.204

Gnomad AMI AF: 0.874

Gnomad AMR AF: 0.795

Gnomad ASJ AF: 0.802

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.901

Gnomad FIN AF: 0.824

Gnomad MID AF: 0.668

Gnomad NFE AF: 0.797

Gnomad OTH AF: 0.669

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: 0.642 AC: 71257 AN: 111025 Hom.: 18647 Cov.: 23 AF XY: 0.657 AC XY: 21855 AN XY: 33283

African (AFR) AF: 0.204 AC: 6261 AN: 30667

American (AMR) AF: 0.795 AC: 8302 AN: 10446

Ashkenazi Jewish (ASJ) AF: 0.802 AC: 2117 AN: 2641

East Asian (EAS) AF: 0.998 AC: 3473 AN: 3480

South Asian (SAS) AF: 0.902 AC: 2347 AN: 2602

European-Finnish (FIN) AF: 0.824 AC: 4852 AN: 5886

Middle Eastern (MID) AF: 0.650 AC: 139 AN: 214

European-Non Finnish (NFE) AF: 0.797 AC: 42150 AN: 52891

Other (OTH) AF: 0.673 AC: 1020 AN: 1516

Alfa AF: 0.748 Hom.: 91268

Bravo AF: 0.627

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.4
DANN	Benign	0.65
PhyloP100		0.41

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs4456006; hg19: chrX-67028222;