rs690346
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_182758.4(WDR72):āc.298A>Gā(p.Met100Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.993 in 1,608,956 control chromosomes in the GnomAD database, including 793,903 homozygotes. 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 Benign (ā ā ).
Frequency
Consequence
NM_182758.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
WDR72 | NM_182758.4 | c.298A>G | p.Met100Val | missense_variant | 4/20 | ENST00000360509.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
WDR72 | ENST00000360509.10 | c.298A>G | p.Met100Val | missense_variant | 4/20 | 1 | NM_182758.4 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.963 AC: 146480AN: 152130Hom.: 70760 Cov.: 33
GnomAD3 exomes AF: 0.990 AC: 248821AN: 251214Hom.: 123361 AF XY: 0.993 AC XY: 134800AN XY: 135762
GnomAD4 exome AF: 0.996 AC: 1451151AN: 1456708Hom.: 723115 Cov.: 36 AF XY: 0.997 AC XY: 722662AN XY: 725032
GnomAD4 genome ? AF: 0.963 AC: 146563AN: 152248Hom.: 70788 Cov.: 33 AF XY: 0.964 AC XY: 71733AN XY: 74434
ClinVar
Submissions by phenotype
Amelogenesis imperfecta hypomaturation type 2A3 Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Dec 05, 2021 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 09, 2021 | - - |
Amelogenesis Imperfecta, Recessive Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at