rs73807272
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001378452.1(ITPR1):c.92+29C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000161 in 1,241,180 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 33)
Exomes 𝑓: 0.0000016 ( 0 hom. )
Consequence
ITPR1
NM_001378452.1 intron
NM_001378452.1 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.139
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 Likely_benign. Variant got -2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.71).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ITPR1 | NM_001378452.1 | c.92+29C>A | intron_variant | Intron 3 of 61 | ENST00000649015.2 | NP_001365381.1 | ||
ITPR1 | NM_001168272.2 | c.92+29C>A | intron_variant | Intron 3 of 60 | NP_001161744.1 | |||
ITPR1 | NM_001099952.4 | c.92+29C>A | intron_variant | Intron 3 of 58 | NP_001093422.2 | |||
ITPR1 | NM_002222.7 | c.92+29C>A | intron_variant | Intron 3 of 57 | NP_002213.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ITPR1 | ENST00000649015.2 | c.92+29C>A | intron_variant | Intron 3 of 61 | NM_001378452.1 | ENSP00000497605.1 | ||||
ITPR1 | ENST00000354582.12 | c.92+29C>A | intron_variant | Intron 3 of 61 | 5 | ENSP00000346595.8 | ||||
ITPR1 | ENST00000648266.1 | c.92+29C>A | intron_variant | Intron 3 of 61 | ENSP00000498014.1 | |||||
ITPR1 | ENST00000650294.1 | c.92+29C>A | intron_variant | Intron 3 of 60 | ENSP00000498056.1 | |||||
ITPR1 | ENST00000443694.5 | c.92+29C>A | intron_variant | Intron 3 of 60 | 1 | ENSP00000401671.2 | ||||
ITPR1 | ENST00000648309.1 | c.92+29C>A | intron_variant | Intron 1 of 58 | ENSP00000497026.1 | |||||
ITPR1 | ENST00000357086.10 | c.92+29C>A | intron_variant | Intron 3 of 58 | 1 | ENSP00000349597.4 | ||||
ITPR1 | ENST00000456211.8 | c.92+29C>A | intron_variant | Intron 3 of 57 | 1 | ENSP00000397885.2 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 genomes
Cov.:
33
GnomAD4 exome AF: 0.00000161 AC: 2AN: 1241180Hom.: 0 Cov.: 17 AF XY: 0.00000319 AC XY: 2AN XY: 627774
GnomAD4 exome
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2
AN:
1241180
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17
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2
AN XY:
627774
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GnomAD4 genome Cov.: 33
GnomAD4 genome
Cov.:
33
Bravo
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ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
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