rs61751570
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 1P and 16B. PP2BP4_StrongBP6_Very_StrongBS2
The NM_001378452.1(ITPR1):āc.3461A>Gā(p.Asp1154Gly) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00143 in 1,613,988 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. D1154Y) has been classified as Uncertain significance.
Frequency
Consequence
NM_001378452.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -15 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ITPR1 | NM_001378452.1 | c.3461A>G | p.Asp1154Gly | missense_variant | 28/62 | ENST00000649015.2 | |
ITPR1 | NM_001168272.2 | c.3416A>G | p.Asp1139Gly | missense_variant | 27/61 | ||
ITPR1 | NM_001099952.4 | c.3434A>G | p.Asp1145Gly | missense_variant | 28/59 | ||
ITPR1 | NM_002222.7 | c.3389A>G | p.Asp1130Gly | missense_variant | 27/58 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ITPR1 | ENST00000649015.2 | c.3461A>G | p.Asp1154Gly | missense_variant | 28/62 | NM_001378452.1 |
Frequencies
GnomAD3 genomes ? AF: 0.00158 AC: 241AN: 152208Hom.: 1 Cov.: 33
GnomAD3 exomes AF: 0.00157 AC: 391AN: 249006Hom.: 1 AF XY: 0.00159 AC XY: 215AN XY: 135074
GnomAD4 exome AF: 0.00141 AC: 2068AN: 1461662Hom.: 3 Cov.: 32 AF XY: 0.00131 AC XY: 950AN XY: 727114
GnomAD4 genome ? AF: 0.00158 AC: 241AN: 152326Hom.: 1 Cov.: 33 AF XY: 0.00191 AC XY: 142AN XY: 74496
ClinVar
Submissions by phenotype
not provided Benign:6
Likely benign, no assertion criteria provided | clinical testing | Genome Diagnostics Laboratory, University Medical Center Utrecht | - | - - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 16, 2021 | This variant is associated with the following publications: (PMID: 29925855) - |
Likely benign, no assertion criteria provided | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | - | - - |
Likely benign, no assertion criteria provided | clinical testing | Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC) | - | - - |
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 25, 2024 | - - |
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Oct 01, 2022 | ITPR1: BS2 - |
Gillespie syndrome;C1847725:Spinocerebellar ataxia type 15/16;C1861732:Spinocerebellar ataxia type 29 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Aug 25, 2021 | - - |
Autosomal dominant cerebellar ataxia Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 13, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. - |
Spinocerebellar ataxia type 29 Benign:1
Likely benign, criteria provided, single submitter | research | Schule lab, Hertie Institute for Clinical Brain Research | Feb 09, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at