chrX-70287312-G-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_016484.5(PDZD11):c.352C>T(p.Arg118Cys) variant causes a missense change. The variant allele was found at a frequency of 0.000167 in 1,206,852 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 53 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. R118H) has been classified as Uncertain significance.
Frequency
Consequence
NM_016484.5 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 |
---|---|---|---|---|---|---|---|
PDZD11 | NM_016484.5 | c.352C>T | p.Arg118Cys | missense_variant | 6/7 | ENST00000239666.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PDZD11 | ENST00000239666.9 | c.352C>T | p.Arg118Cys | missense_variant | 6/7 | 1 | NM_016484.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000813 AC: 9AN: 110753Hom.: 0 Cov.: 23 AF XY: 0.000121 AC XY: 4AN XY: 33015
GnomAD3 exomes AF: 0.0000877 AC: 16AN: 182477Hom.: 0 AF XY: 0.0000747 AC XY: 5AN XY: 66957
GnomAD4 exome AF: 0.000175 AC: 192AN: 1096099Hom.: 0 Cov.: 29 AF XY: 0.000136 AC XY: 49AN XY: 361525
GnomAD4 genome ? AF: 0.0000813 AC: 9AN: 110753Hom.: 0 Cov.: 23 AF XY: 0.000121 AC XY: 4AN XY: 33015
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 21, 2023 | The c.352C>T (p.R118C) alteration is located in exon 6 (coding exon 5) of the PDZD11 gene. This alteration results from a C to T substitution at nucleotide position 352, causing the arginine (R) at amino acid position 118 to be replaced by a cysteine (C). 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