X-153804029-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_001303512.2(PDZD4):c.1652G>A(p.Arg551His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000225 in 1,157,052 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 7 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001303512.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PDZD4 | ENST00000393758.7 | c.1652G>A | p.Arg551His | missense_variant | Exon 8 of 8 | 1 | NM_001303512.2 | ENSP00000377355.3 | ||
PDZD4 | ENST00000164640.8 | c.1634G>A | p.Arg545His | missense_variant | Exon 8 of 8 | 1 | ENSP00000164640.4 | |||
PDZD4 | ENST00000544474.5 | c.1307G>A | p.Arg436His | missense_variant | Exon 6 of 6 | 1 | ENSP00000442033.1 |
Frequencies
GnomAD3 genomes AF: 0.0000615 AC: 7AN: 113729Hom.: 0 Cov.: 25 AF XY: 0.0000558 AC XY: 2AN XY: 35867
GnomAD3 exomes AF: 0.0000333 AC: 3AN: 90205Hom.: 0 AF XY: 0.0000333 AC XY: 1AN XY: 30061
GnomAD4 exome AF: 0.0000182 AC: 19AN: 1043323Hom.: 0 Cov.: 33 AF XY: 0.0000148 AC XY: 5AN XY: 338813
GnomAD4 genome AF: 0.0000615 AC: 7AN: 113729Hom.: 0 Cov.: 25 AF XY: 0.0000558 AC XY: 2AN XY: 35867
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1634G>A (p.R545H) alteration is located in exon 8 (coding exon 8) of the PDZD4 gene. This alteration results from a G to A substitution at nucleotide position 1634, causing the arginine (R) at amino acid position 545 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