chrX-153804122-G-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_ModerateBP6_ModerateBS2
The NM_001303512.2(PDZD4):c.1559C>A(p.Pro520His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00002 in 1,150,583 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 8 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P520R) has been classified as Uncertain significance.
Frequency
Consequence
NM_001303512.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PDZD4 | NM_001303512.2 | c.1559C>A | p.Pro520His | missense_variant | 8/8 | ENST00000393758.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PDZD4 | ENST00000393758.7 | c.1559C>A | p.Pro520His | missense_variant | 8/8 | 1 | NM_001303512.2 | P4 | |
PDZD4 | ENST00000164640.8 | c.1541C>A | p.Pro514His | missense_variant | 8/8 | 1 | A1 | ||
PDZD4 | ENST00000544474.5 | c.1214C>A | p.Pro405His | missense_variant | 6/6 | 1 |
Frequencies
GnomAD3 genomes AF: 0.00000882 AC: 1AN: 113393Hom.: 0 Cov.: 26 AF XY: 0.00 AC XY: 0AN XY: 35539
GnomAD4 exome AF: 0.0000212 AC: 22AN: 1037190Hom.: 0 Cov.: 33 AF XY: 0.0000239 AC XY: 8AN XY: 334308
GnomAD4 genome AF: 0.00000882 AC: 1AN: 113393Hom.: 0 Cov.: 26 AF XY: 0.00 AC XY: 0AN XY: 35539
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at