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NM_002180.3(IGHMBP2):c.2369G>A (p.Arg790Gln)

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Interpretation:
Conflicting interpretations of pathogenicity​

Likely benign(1);Uncertain significance(4)

Review status:
criteria provided, conflicting interpretations
Submissions:
5 (Most recent: Sep 25, 2021)
Last evaluated:
Jun 18, 2021
Accession:
VCV000245632.16
Variation ID:
245632
Description:
single nucleotide variant
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NM_002180.3(IGHMBP2):c.2369G>A (p.Arg790Gln)

Allele ID
244691
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
11q13.3
Genomic location
11: 68936849 (GRCh38) GRCh38 UCSC
11: 68704317 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
LRG_250:g.37999G>A
LRG_250t1:c.2369G>A LRG_250p1:p.Arg790Gln
NC_000011.10:g.68936849G>A
... more HGVS
Protein change
R790Q
Other names
-
Canonical SPDI
NC_000011.10:68936848:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
0.00020 (A)

Allele frequency
1000 Genomes Project 0.00020
The Genome Aggregation Database (gnomAD) 0.00013
The Genome Aggregation Database (gnomAD) 0.00026
The Genome Aggregation Database (gnomAD), exomes 0.00034
Trans-Omics for Precision Medicine (TOPMed) 0.00034
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00031
Trans-Omics for Precision Medicine (TOPMed) 0.00033
Exome Aggregation Consortium (ExAC) 0.00043
Links
ClinGen: CA6153897
dbSNP: rs147038490
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Uncertain significance 2 criteria provided, multiple submitters, no conflicts Jun 18, 2021 RCV000235815.5
Likely benign 1 criteria provided, single submitter Sep 3, 2020 RCV000547188.6
Uncertain significance 1 criteria provided, single submitter Jan 13, 2018 RCV001110520.1
Uncertain significance 1 criteria provided, single submitter Nov 20, 2019 RCV001285918.2
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
IGHMBP2 - - GRCh38
GRCh37
823 839

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Uncertain significance
(Jun 18, 2021)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000292591.10
Submitted: (Sep 25, 2021)
Evidence details
Comment:
In silico analysis supports that this missense variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge; … (more)
Uncertain significance
(Jan 13, 2018)
criteria provided, single submitter
Method: clinical testing
Spinal muscular atrophy, distal, autosomal recessive, 1
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV001267969.1
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)
Uncertain significance
(Nov 20, 2019)
criteria provided, single submitter
Method: clinical testing
none provided
Allele origin: germline
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories
Accession: SCV001472427.1
Submitted: (Dec 11, 2020)
Evidence details
Likely benign
(Sep 03, 2020)
criteria provided, single submitter
Method: clinical testing
Spinal muscular atrophy, distal, autosomal recessive, 1
Charcot-Marie-Tooth disease, axonal, type 2S
Allele origin: germline
Invitae
Accession: SCV000642338.6
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (1)
Uncertain significance
(Nov 01, 2016)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
CeGaT Praxis fuer Humangenetik Tuebingen
Accession: SCV001148363.7
Submitted: (Jul 04, 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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Title Author Journal Year Link
Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. Nykamp K Genetics in medicine : official journal of the American College of Medical Genetics 2017 PMID: 28492532

Text-mined citations for rs147038490...

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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 Dec 04, 2021