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NM_002180.3(IGHMBP2):c.2782G>A (p.Glu928Lys)

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Interpretation:
Benign​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
8 (Most recent: Sep 23, 2021)
Last evaluated:
Dec 7, 2020
Accession:
VCV000258573.8
Variation ID:
258573
Description:
single nucleotide variant
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NM_002180.3(IGHMBP2):c.2782G>A (p.Glu928Lys)

Allele ID
254309
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
11q13.3
Genomic location
11: 68938352 (GRCh38) GRCh38 UCSC
11: 68705820 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
LRG_250:g.39502G>A
LRG_250t1:c.2782G>A LRG_250p1:p.Glu928Lys
P38935:p.Glu928Lys
... more HGVS
Protein change
E928K
Other names
-
Canonical SPDI
NC_000011.10:68938351:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
0.02356 (A)

Allele frequency
The Genome Aggregation Database (gnomAD) 0.00637
The Genome Aggregation Database (gnomAD) 0.00707
Trans-Omics for Precision Medicine (TOPMed) 0.01109
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00193
Trans-Omics for Precision Medicine (TOPMed) 0.01266
The Genome Aggregation Database (gnomAD), exomes 0.01849
Exome Aggregation Consortium (ExAC) 0.02034
1000 Genomes Project 0.02356
Links
ClinGen: CA6154002
UniProtKB: P38935#VAR_021900
dbSNP: rs2275996
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign 3 criteria provided, multiple submitters, no conflicts Sep 20, 2017 RCV000712264.4
Benign 2 criteria provided, single submitter - RCV000244618.2
Benign 1 criteria provided, single submitter Jan 13, 2018 RCV000288957.2
Benign 1 criteria provided, single submitter Dec 7, 2020 RCV000554374.3
Benign 1 criteria provided, single submitter - RCV001173369.1
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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
822 838

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Benign
(-)
criteria provided, single submitter
Method: clinical testing
NOT SPECIFIED
Allele origin: germline
PreventionGenetics,PreventionGenetics
Accession: SCV000308728.1
Submitted: (Apr 28, 2016)
Evidence details
Benign
(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: SCV000373808.3
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 20, 2017)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Athena Diagnostics Inc
Accession: SCV000842710.1
Submitted: (Aug 31, 2018)
Evidence details
Publications
PubMed (2)
Benign
(-)
criteria provided, single submitter
Method: clinical testing
Charcot-Marie-Tooth disease
Allele origin: germline
Molecular Genetics Laboratory,London Health Sciences Centre
Accession: SCV001336457.1
Submitted: (Apr 07, 2020)
Evidence details
Benign
(Dec 07, 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: SCV000642350.3
Submitted: (Jan 07, 2021)
Evidence details
Benign
(Mar 03, 2015)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV001900861.1
Submitted: (Sep 19, 2021)
Evidence details
Likely benign
(-)
no assertion criteria provided
Method: clinical testing
not provided
Allele origin: germline
Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC)
Study: VKGL Data-share Consensus
Accession: SCV001797379.1
Submitted: (Aug 19, 2021)
Evidence details
Benign
(-)
no assertion criteria provided
Method: clinical testing
not specified
Allele origin: germline
Clinical Genetics,Academic Medical Center
Additional submitter:
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001921073.1
Submitted: (Sep 23, 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
Variation in IGHMBP2 is not associated with IgA nephropathy in independent studies of UK Caucasian and Chinese Han patients. Lou T Nephrology, dialysis, transplantation : official publication of the European Dialysis and Transplant Association - European Renal Association 2010 PMID: 20031928
Association of a single-nucleotide polymorphism in the immunoglobulin mu-binding protein 2 gene with immunoglobulin A nephropathy. Ohtsubo S Journal of human genetics 2005 PMID: 15599641

Text-mined citations for rs2275996...

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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 Nov 27, 2021