NM_002180.2(IGHMBP2):c.1071C>T (p.Ala357=) AND not provided

Clinical significance:Likely benign (Last evaluated: Mar 25, 2018)

Review status:2 stars out of maximum of 4 stars

criteria provided, multiple submitters, no conflicts

Based on:
2 submissions [Details]
Record status:
current
Accession:
RCV000756268.2

Allele description [Variation Report for NM_002180.2(IGHMBP2):c.1071C>T (p.Ala357=)]

NM_002180.2(IGHMBP2):c.1071C>T (p.Ala357=)

Gene:
IGHMBP2:immunoglobulin mu DNA binding protein 2 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
11q13.3
Genomic location:
Preferred name:
NM_002180.2(IGHMBP2):c.1071C>T (p.Ala357=)
HGVS:
  • NC_000011.10:g.68929193C>T
  • NG_007976.1:g.30343C>T
  • NM_002180.2:c.1071C>T
  • NP_002171.2:p.Ala357=
  • LRG_250t1:c.1071C>T
  • LRG_250:g.30343C>T
  • LRG_250p1:p.Ala357=
  • NC_000011.9:g.68696661C>T
  • p.Ala357Ala
Links:
dbSNP: rs755300047
NCBI 1000 Genomes Browser:
rs755300047
Molecular consequence:
  • NM_002180.2:c.1071C>T - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

Identifiers:
MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000884026ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratoriescriteria provided, single submitter
Likely benign
(Mar 7, 2018)
germlineclinical testing

Citation Link,

SCV001079421Invitaecriteria provided, single submitter
Likely benign
(Mar 25, 2018)
germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240-242.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories, SCV000884026.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

The c.1071C>T; p.Ala357Ala variant (rs755300047) does not alter the amino acid sequence of the IGHMBP2 protein and computational splice site prediction algorithms do not predict a change in the nearest splice site or creation of a cryptic splice site. This variant has not been reported in association with CMT or neuropathy in medical literature or in gene specific variation databases. This variant is listed in the genome Aggregation Database (gnomAD) with an overall population frequency of 0.002% (identified on 4 out of 245,292 chromosomes). Based on the available information, the c.1071C>T variant is likely to be benign.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Invitae, SCV001079421.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: May 26, 2021

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