rs144081442
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_ModerateBP6_ModerateBS2
The NM_001029896.2(WDR45):c.398G>A(p.Arg133Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000019 in 1,210,487 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 6 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 Likely benign (★).
Frequency
Consequence
NM_001029896.2 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 |
---|---|---|---|---|---|---|---|
WDR45 | NM_001029896.2 | c.398G>A | p.Arg133Gln | missense_variant | 6/11 | ENST00000376372.9 | |
WDR45 | NM_007075.4 | c.401G>A | p.Arg134Gln | missense_variant | 7/12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
WDR45 | ENST00000376372.9 | c.398G>A | p.Arg133Gln | missense_variant | 6/11 | 1 | NM_001029896.2 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000534 AC: 6AN: 112362Hom.: 0 Cov.: 23 AF XY: 0.0000290 AC XY: 1AN XY: 34520
GnomAD3 exomes AF: 0.00000545 AC: 1AN: 183450Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 67898
GnomAD4 exome AF: 0.0000155 AC: 17AN: 1098125Hom.: 0 Cov.: 31 AF XY: 0.0000138 AC XY: 5AN XY: 363513
GnomAD4 genome ? AF: 0.0000534 AC: 6AN: 112362Hom.: 0 Cov.: 23 AF XY: 0.0000290 AC XY: 1AN XY: 34520
ClinVar
Submissions by phenotype
Neurodegeneration with brain iron accumulation 5 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Sep 04, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at