chrX-70287311-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_016484.5(PDZD11):c.353G>A(p.Arg118His) variant causes a missense change. The variant allele was found at a frequency of 0.00000497 in 1,206,829 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 1 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R118C) has been classified as Uncertain significance.
Frequency
Consequence
NM_016484.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PDZD11 | NM_016484.5 | c.353G>A | p.Arg118His | missense_variant | 6/7 | ENST00000239666.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PDZD11 | ENST00000239666.9 | c.353G>A | p.Arg118His | missense_variant | 6/7 | 1 | NM_016484.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000905 AC: 1AN: 110486Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0AN XY: 32856
GnomAD4 exome AF: 0.00000456 AC: 5AN: 1096343Hom.: 0 Cov.: 29 AF XY: 0.00000276 AC XY: 1AN XY: 361753
GnomAD4 genome ? AF: 0.00000905 AC: 1AN: 110486Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0AN XY: 32856
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 16, 2022 | The c.353G>A (p.R118H) alteration is located in exon 6 (coding exon 5) of the PDZD11 gene. This alteration results from a G to A substitution at nucleotide position 353, causing the arginine (R) at amino acid position 118 to be replaced by a histidine (H). 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