rs11146013
Positions:
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The NM_019892.6(INPP5E):c.1549+40G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00024 ( 0 hom., cov: 9)
Exomes 𝑓: 0.00011 ( 1 hom. )
Consequence
INPP5E
NM_019892.6 intron
NM_019892.6 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.323
Genes affected
INPP5E (HGNC:21474): (inositol polyphosphate-5-phosphatase E) The protein encoded by this gene is an inositol 1,4,5-trisphosphate (InsP3) 5-phosphatase. InsP3 5-phosphatases hydrolyze Ins(1,4,5)P3, which mobilizes intracellular calcium and acts as a second messenger mediating cell responses to various stimulation. Studies of the mouse counterpart suggest that this protein may hydrolyze phosphatidylinositol 3,4,5-trisphosphate and phosphatidylinositol 3,5-bisphosphate on the cytoplasmic Golgi membrane and thereby regulate Golgi-vesicular trafficking. Mutations in this gene cause Joubert syndrome; a clinically and genetically heterogenous group of disorders characterized by midbrain-hindbrain malformation and various associated ciliopathies that include retinal dystrophy, nephronophthisis, liver fibrosis and polydactyly. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jan 2016]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -6 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.94).
BP6
?
Variant 9-136431784-C-T is Benign according to our data. Variant chr9-136431784-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 261198.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
INPP5E | NM_019892.6 | c.1549+40G>A | intron_variant | ENST00000371712.4 | |||
INPP5E | NM_001318502.2 | c.1546+40G>A | intron_variant | ||||
INPP5E | XM_017014926.2 | c.1549+40G>A | intron_variant | ||||
INPP5E | XM_047423603.1 | c.1546+40G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
INPP5E | ENST00000371712.4 | c.1549+40G>A | intron_variant | 1 | NM_019892.6 | P1 | |||
INPP5E | ENST00000676019.1 | c.1447+40G>A | intron_variant |
Frequencies
GnomAD3 genomes ? AF: 0.000237 AC: 14AN: 58998Hom.: 0 Cov.: 9
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GnomAD3 exomes AF: 0.0000637 AC: 10AN: 157032Hom.: 0 AF XY: 0.0000462 AC XY: 4AN XY: 86630
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GnomAD4 exome AF: 0.000111 AC: 94AN: 849992Hom.: 1 Cov.: 15 AF XY: 0.000107 AC XY: 46AN XY: 431876
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GnomAD4 genome ? AF: 0.000237 AC: 14AN: 59020Hom.: 0 Cov.: 9 AF XY: 0.000179 AC XY: 5AN XY: 27940
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
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Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at