17-49600402-TG-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001007228.2(SPOP):c.1100del(p.Pro367HisfsTer5) variant causes a frameshift change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. P367P) has been classified as Likely benign.
Frequency
Consequence
NM_001007228.2 frameshift
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SPOP | NM_001007228.2 | c.1100del | p.Pro367HisfsTer5 | frameshift_variant | 10/10 | ENST00000504102.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SPOP | ENST00000504102.6 | c.1100del | p.Pro367HisfsTer5 | frameshift_variant | 10/10 | 1 | NM_001007228.2 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome Cov.: 31
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
Neurodevelopmental disorder with microcephaly and dysmorphic facies Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Clinical Genomics Laboratory, Washington University in St. Louis | Apr 12, 2024 | The SPOP c.1100del (p.Pro367Hisfs*5) variant, to our knowledge, has not been reported in the medical literature and is absent from the general population (gnomAD v.2.1.1), indicating it is not a common variant. This variant causes a frameshift by deleting a single nucleotide, leading to a premature termination codon; however, because this occurs in the last exon and is only predicted to delete eight amino acids, this is not predicted to lead to nonsense mediated decay. One publication indicates a nuclear localization signal may be located in the amino acids that would be deleted due to this variation (Shi Q et al., PMID: 31771591), but another publication indicates the nuclear localization signal is in another region (Nagai Y et al., PMID: 9414087). Due to limited information, and based on ACMG/AMP guidelines for variant interpretation (Richards S et al., PMID: 25741868), the clinical significance of this variant is uncertain at this time. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.