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NM_001378452.1(ITPR1):c.6717A>G (p.Thr2239=)

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Interpretation:
Benign​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
7 (Most recent: Sep 21, 2021)
Last evaluated:
Dec 8, 2020
Accession:
VCV000129301.12
Variation ID:
129301
Description:
single nucleotide variant
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NM_001378452.1(ITPR1):c.6717A>G (p.Thr2239=)

Allele ID
134747
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
3p26.1
Genomic location
3: 4788048 (GRCh38) GRCh38 UCSC
3: 4829732 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000003.11:g.4829732A>G
NM_001168272.1:c.6672A>G NP_001161744.1:p.Thr2224= synonymous
NC_000003.12:g.4788048A>G
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000003.12:4788047:A:G
Functional consequence
-
Global minor allele frequency (GMAF)
0.24561 (G)

Allele frequency
1000 Genomes Project 0.24561
Trans-Omics for Precision Medicine (TOPMed) 0.29241
Exome Aggregation Consortium (ExAC) 0.32942
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.30488
The Genome Aggregation Database (gnomAD), exomes 0.30087
The Genome Aggregation Database (gnomAD) 0.31962
Links
ClinGen: CA153219
dbSNP: rs13079522
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign 2 criteria provided, multiple submitters, no conflicts Dec 8, 2020 RCV001521932.4
Benign 4 criteria provided, single submitter Sep 4, 2019 RCV000117302.7
Benign 1 criteria provided, single submitter Jan 12, 2018 RCV000404506.2
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
ITPR1 - - GRCh38
GRCh37
795 888

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Benign
(Jan 12, 2018)
criteria provided, single submitter
Method: clinical testing
Spinocerebellar Ataxia, Dominant
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000444986.3
Submitted: (Feb 20, 2020)
Evidence details
Comment:
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 … (more)
Benign
(Sep 04, 2019)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: unknown
Athena Diagnostics Inc
Accession: SCV001475927.1
Submitted: (Dec 30, 2020)
Evidence details
Benign
(Dec 08, 2020)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Invitae
Accession: SCV001731369.1
Submitted: (Jan 07, 2021)
Evidence details
Benign
(Jul 26, 2018)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV001842316.1
Submitted: (Sep 08, 2021)
Evidence details
Likely benign
(-)
no assertion criteria provided
Method: clinical testing
AllHighlyPenetrant
(Autosomal dominant inheritance)
Allele origin: germline
Genetic Services Laboratory,University of Chicago
Accession: SCV000151483.2
Submitted: (Jun 27, 2014)
Evidence details
Comment:
Likely benign based on allele frequency in 1000 Genomes Project or ESP global frequency and its presence in a patient with a rare or unrelated … (more)
Benign
(-)
no assertion criteria provided
Method: clinical testing
not specified
Allele origin: germline
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001742063.3
Submitted: (Sep 02, 2021)
Evidence details
Benign
(-)
no assertion criteria provided
Method: clinical testing
not specified
Allele origin: germline
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center
Additional submitter:
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001975379.1
Submitted: (Sep 21, 2021)
Evidence details

Functional evidence

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There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

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There are no citations in ClinVar for this variation. If you know of citations for this variation, please consider submitting that information to ClinVar.

Text-mined citations for rs13079522...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Oct 30, 2021