rs6442905
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Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_001378452.1(ITPR1):āc.6111T>Cā(p.Asn2037=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.971 in 1,613,740 control chromosomes in the GnomAD database, including 761,111 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ).
Frequency
Genomes: š 0.97 ( 71220 hom., cov: 32)
Exomes š: 0.97 ( 689891 hom. )
Consequence
ITPR1
NM_001378452.1 synonymous
NM_001378452.1 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -3.09
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 -21 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.67).
BP6
?
Variant 3-4775373-T-C is Benign according to our data. Variant chr3-4775373-T-C is described in ClinVar as [Benign]. Clinvar id is 1170008.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-4775373-T-C is described in Lovd as [Benign].
BP7
?
Synonymous conserved (PhyloP=-3.09 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.965 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ITPR1 | NM_001378452.1 | c.6111T>C | p.Asn2037= | synonymous_variant | 47/62 | ENST00000649015.2 | |
ITPR1 | NM_001168272.2 | c.6066T>C | p.Asn2022= | synonymous_variant | 46/61 | ||
ITPR1 | NM_001099952.4 | c.5967T>C | p.Asn1989= | synonymous_variant | 44/59 | ||
ITPR1 | NM_002222.7 | c.5922T>C | p.Asn1974= | synonymous_variant | 43/58 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ITPR1 | ENST00000649015.2 | c.6111T>C | p.Asn2037= | synonymous_variant | 47/62 | NM_001378452.1 |
Frequencies
GnomAD3 genomes ? AF: 0.967 AC: 147172AN: 152216Hom.: 71164 Cov.: 32
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GnomAD3 exomes AF: 0.971 AC: 242087AN: 249286Hom.: 117599 AF XY: 0.970 AC XY: 131193AN XY: 135234
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GnomAD4 exome AF: 0.972 AC: 1419914AN: 1461406Hom.: 689891 Cov.: 44 AF XY: 0.971 AC XY: 706047AN XY: 727034
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GnomAD4 genome ? AF: 0.967 AC: 147287AN: 152334Hom.: 71220 Cov.: 32 AF XY: 0.967 AC XY: 72066AN XY: 74490
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ClinVar
Significance: Benign
Submissions summary: Benign:6
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:2
Benign, no assertion criteria provided | clinical testing | Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen | - | - - |
Benign, no assertion criteria provided | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | - | - - |
Gillespie syndrome Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Aug 19, 2021 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
Spinocerebellar ataxia type 29 Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Aug 19, 2021 | - - |
Spinocerebellar ataxia type 15/16 Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Aug 19, 2021 | - - |
Computational scores
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Name
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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