rs304075
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The NM_001378452.1(ITPR1):c.-93+141G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0289 in 152,416 control chromosomes in the GnomAD database, including 92 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.029 ( 92 hom., cov: 32)
Exomes 𝑓: 0.052 ( 0 hom. )
Consequence
ITPR1
NM_001378452.1 intron
NM_001378452.1 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.458
Genes affected
ITPR1 (HGNC:6180): (inositol 1,4,5-trisphosphate receptor type 1) This gene encodes an intracellular receptor for inositol 1,4,5-trisphosphate. Upon stimulation by inositol 1,4,5-trisphosphate, this receptor mediates calcium release from the endoplasmic reticulum. Mutations in this gene cause spinocerebellar ataxia type 15, a disease associated with an heterogeneous group of cerebellar disorders. Multiple transcript variants have been identified for this gene. [provided by RefSeq, Nov 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.78).
BS1
?
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0288 (4392/152282) while in subpopulation NFE AF= 0.0464 (3153/68016). AF 95% confidence interval is 0.045. There are 92 homozygotes in gnomad4. There are 2017 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd4 at 92 AD,AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ITPR1 | NM_001378452.1 | c.-93+141G>A | intron_variant | ENST00000649015.2 | |||
ITPR1 | NM_001099952.4 | c.-93+141G>A | intron_variant | ||||
ITPR1 | NM_001168272.2 | c.-93+141G>A | intron_variant | ||||
ITPR1 | NM_002222.7 | c.-93+141G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ITPR1 | ENST00000649015.2 | c.-93+141G>A | intron_variant | NM_001378452.1 |
Frequencies
GnomAD3 genomes ? AF: 0.0289 AC: 4390AN: 152164Hom.: 92 Cov.: 32
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GnomAD4 exome AF: 0.0522 AC: 7AN: 134Hom.: 0 AF XY: 0.0463 AC XY: 5AN XY: 108
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GnomAD4 genome ? AF: 0.0288 AC: 4392AN: 152282Hom.: 92 Cov.: 32 AF XY: 0.0271 AC XY: 2017AN XY: 74468
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ClinVar
Not reported inComputational scores
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Name
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Prediction
BayesDel_noAF
Benign
CADD
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