chrX-91878347-A-G
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_032968.5(PCDH11X):c.2107A>G(p.Asn703Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000324 in 1,204,836 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 9 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_032968.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PCDH11X | NM_032968.5 | c.2107A>G | p.Asn703Asp | missense_variant | 6/11 | ENST00000682573.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PCDH11X | ENST00000682573.1 | c.2107A>G | p.Asn703Asp | missense_variant | 6/11 | NM_032968.5 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000185 AC: 2AN: 108330Hom.: 0 Cov.: 20 AF XY: 0.00 AC XY: 0AN XY: 30594
GnomAD3 exomes AF: 0.0000164 AC: 3AN: 182782Hom.: 0 AF XY: 0.0000296 AC XY: 2AN XY: 67556
GnomAD4 exome AF: 0.0000337 AC: 37AN: 1096506Hom.: 0 Cov.: 30 AF XY: 0.0000249 AC XY: 9AN XY: 361992
GnomAD4 genome ? AF: 0.0000185 AC: 2AN: 108330Hom.: 0 Cov.: 20 AF XY: 0.00 AC XY: 0AN XY: 30594
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 28, 2023 | The c.2107A>G (p.N703D) alteration is located in exon 2 (coding exon 2) of the PCDH11X gene. This alteration results from a A to G substitution at nucleotide position 2107, causing the asparagine (N) at amino acid position 703 to be replaced by an aspartic acid (D). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at