rs2573905
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong
The NM_032968.5(PCDH11X):c.3034-54154T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.0 ( 0 hom., 0 hem., cov: 20)
Failed GnomAD Quality Control
Consequence
PCDH11X
NM_032968.5 intron
NM_032968.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.135
Publications
15 publications found
Genes affected
PCDH11X (HGNC:8656): (protocadherin 11 X-linked) This gene belongs to the protocadherin gene family, a subfamily of the cadherin superfamily. The encoded protein consists of an extracellular domain containing 7 cadherin repeats, a transmembrane domain and a cytoplasmic tail that differs from those of the classical cadherins. The gene is located in a major X/Y block of homology and its Y homolog, despite divergence leading to coding region changes, is the most closely related cadherin family member. The protein is thought to play a fundamental role in cell-cell recognition essential for the segmental development and function of the central nervous system. Disruption of this gene may be associated with developmental dyslexia. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jun 2014]
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -4 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.93).
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_032968.5. You can select a different transcript below to see updated ACMG assignments.
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| PCDH11X | MANE Select | c.3034-54154T>A | intron | N/A | ENSP00000507225.1 | Q9BZA7-1 | |||
| PCDH11X | TSL:1 | c.3034-54154T>A | intron | N/A | ENSP00000362186.1 | Q9BZA7-1 | |||
| PCDH11X | TSL:1 | c.3034-54154T>A | intron | N/A | ENSP00000384758.1 | Q9BZA7-8 |
Frequencies
GnomAD3 genomes 0.00 AC: 0AN: 106593Hom.: 0 Cov.: 20
GnomAD3 genomes
AF:
AC:
0
AN:
106593
Hom.:
Cov.:
20
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome 0.00 AC: 0AN: 106593Hom.: 0 Cov.: 20 AF XY: 0.00 AC XY: 0AN XY: 29321
GnomAD4 genome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
106593
Hom.:
Cov.:
20
AF XY:
AC XY:
0
AN XY:
29321
African (AFR)
AF:
AC:
0
AN:
28102
American (AMR)
AF:
AC:
0
AN:
10050
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
2615
East Asian (EAS)
AF:
AC:
0
AN:
3492
South Asian (SAS)
AF:
AC:
0
AN:
2475
European-Finnish (FIN)
AF:
AC:
0
AN:
5487
Middle Eastern (MID)
AF:
AC:
0
AN:
230
European-Non Finnish (NFE)
AF:
AC:
0
AN:
52066
Other (OTH)
AF:
AC:
0
AN:
1424
Alfa
AF:
Hom.:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.