X-91878301-G-A
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2
The NM_032968.5(PCDH11X):c.2061G>A(p.Pro687=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0017 in 1,208,256 control chromosomes in the GnomAD database, including 14 homozygotes. There are 576 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0074 ( 5 hom., 220 hem., cov: 20)
Exomes 𝑓: 0.0011 ( 9 hom. 356 hem. )
Consequence
PCDH11X
NM_032968.5 synonymous
NM_032968.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.458
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -15 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.78).
BP6
?
Variant X-91878301-G-A is Benign according to our data. Variant chrX-91878301-G-A is described in ClinVar as [Benign]. Clinvar id is 787161.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=0.458 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00744 (820/110167) while in subpopulation AFR AF= 0.0231 (698/30272). AF 95% confidence interval is 0.0216. There are 5 homozygotes in gnomad4. There are 220 alleles in male gnomad4 subpopulation. Median coverage is 20. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 5 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PCDH11X | NM_032968.5 | c.2061G>A | p.Pro687= | synonymous_variant | 6/11 | ENST00000682573.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PCDH11X | ENST00000682573.1 | c.2061G>A | p.Pro687= | synonymous_variant | 6/11 | NM_032968.5 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.00743 AC: 818AN: 110111Hom.: 5 Cov.: 20 AF XY: 0.00674 AC XY: 218AN XY: 32343
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GnomAD3 exomes AF: 0.00232 AC: 426AN: 183279Hom.: 6 AF XY: 0.00177 AC XY: 120AN XY: 67847
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GnomAD4 exome AF: 0.00112 AC: 1231AN: 1098089Hom.: 9 Cov.: 31 AF XY: 0.000979 AC XY: 356AN XY: 363565
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at