9-136433147-G-GCGCCCACCCCTTCAGCCGCGCCCACCCCTCCAGCCA
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_019892.6(INPP5E):c.1159+7_1159+8insTGGCTGGAGGGGTGGGCGCGGCTGAAGGGGTGGGCG variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_019892.6 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
INPP5E | ENST00000371712.4 | c.1159+7_1159+8insTGGCTGGAGGGGTGGGCGCGGCTGAAGGGGTGGGCG | splice_region_variant, intron_variant | Intron 4 of 9 | 1 | NM_019892.6 | ENSP00000360777.3 | |||
INPP5E | ENST00000676019.1 | c.1057+7_1057+8insTGGCTGGAGGGGTGGGCGCGGCTGAAGGGGTGGGCG | splice_region_variant, intron_variant | Intron 4 of 9 | ENSP00000501984.1 |
Frequencies
GnomAD3 genomes Cov.: 28
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000207 AC: 3AN: 1452220Hom.: 0 Cov.: 53 AF XY: 0.00000277 AC XY: 2AN XY: 722672
GnomAD4 genome Cov.: 28
ClinVar
Submissions by phenotype
Familial aplasia of the vermis Uncertain:1
This sequence change falls in intron 4 of the INPP5E gene. It does not directly change the encoded amino acid sequence of the INPP5E protein. This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with INPP5E-related conditions. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.