3-4516554-A-C
Variant names:
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_StrongBP6_ModerateBP7
The NM_001378452.1(ITPR1):āc.63A>Cā(p.Gly21Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000112 in 1,605,092 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ).
Frequency
Genomes: š 0.0000066 ( 0 hom., cov: 33)
Exomes š: 0.000012 ( 0 hom. )
Consequence
ITPR1
NM_001378452.1 synonymous
NM_001378452.1 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.239
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 -7 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.52).
BP6
Variant 3-4516554-A-C is Benign according to our data. Variant chr3-4516554-A-C is described in ClinVar as [Likely_benign]. Clinvar id is 3670681.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=0.239 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ITPR1 | NM_001378452.1 | c.63A>C | p.Gly21Gly | synonymous_variant | Exon 3 of 62 | ENST00000649015.2 | NP_001365381.1 | |
ITPR1 | NM_001168272.2 | c.63A>C | p.Gly21Gly | synonymous_variant | Exon 3 of 61 | NP_001161744.1 | ||
ITPR1 | NM_001099952.4 | c.63A>C | p.Gly21Gly | synonymous_variant | Exon 3 of 59 | NP_001093422.2 | ||
ITPR1 | NM_002222.7 | c.63A>C | p.Gly21Gly | synonymous_variant | Exon 3 of 58 | NP_002213.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ITPR1 | ENST00000649015.2 | c.63A>C | p.Gly21Gly | synonymous_variant | Exon 3 of 62 | NM_001378452.1 | ENSP00000497605.1 | |||
ITPR1 | ENST00000354582.12 | c.63A>C | p.Gly21Gly | synonymous_variant | Exon 3 of 62 | 5 | ENSP00000346595.8 | |||
ITPR1 | ENST00000648266.1 | c.63A>C | p.Gly21Gly | synonymous_variant | Exon 3 of 62 | ENSP00000498014.1 | ||||
ITPR1 | ENST00000650294.1 | c.63A>C | p.Gly21Gly | synonymous_variant | Exon 3 of 61 | ENSP00000498056.1 | ||||
ITPR1 | ENST00000443694.5 | c.63A>C | p.Gly21Gly | synonymous_variant | Exon 3 of 61 | 1 | ENSP00000401671.2 | |||
ITPR1 | ENST00000648309.1 | c.63A>C | p.Gly21Gly | synonymous_variant | Exon 1 of 59 | ENSP00000497026.1 | ||||
ITPR1 | ENST00000357086.10 | c.63A>C | p.Gly21Gly | synonymous_variant | Exon 3 of 59 | 1 | ENSP00000349597.4 | |||
ITPR1 | ENST00000456211.8 | c.63A>C | p.Gly21Gly | synonymous_variant | Exon 3 of 58 | 1 | ENSP00000397885.2 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152210Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.00000412 AC: 1AN: 242600Hom.: 0 AF XY: 0.00000758 AC XY: 1AN XY: 131848
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GnomAD4 exome AF: 0.0000117 AC: 17AN: 1452882Hom.: 0 Cov.: 28 AF XY: 0.0000125 AC XY: 9AN XY: 722628
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GnomAD4 genome AF: 0.00000657 AC: 1AN: 152210Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74366
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Jun 17, 2024
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
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Computational scores
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Name
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Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at