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NM_001370259.2(MEN1):c.-6G>A AND not specified

Clinical significance:Benign/Likely benign (Last evaluated: Jan 11, 2022)

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:
RCV001820028.5

Allele description [Variation Report for NM_001370259.2(MEN1):c.-6G>A]

NM_001370259.2(MEN1):c.-6G>A

Gene:
MEN1:menin 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
11q13.1
Genomic location:
Preferred name:
NM_001370259.2(MEN1):c.-6G>A
HGVS:
  • NC_000011.10:g.64810115C>T
  • NG_008929.1:g.6180G>A
  • NM_000244.4:c.-6G>A
  • NM_001370251.2:c.-6G>A
  • NM_001370259.2:c.-6G>AMANE SELECT
  • NM_001370260.2:c.-6G>A
  • NM_001370261.2:c.-6G>A
  • NM_001370262.2:c.-6G>A
  • NM_001370263.2:c.-6G>A
  • NM_130799.3:c.-6G>A
  • NM_130800.3:c.-6G>A
  • NM_130801.3:c.-6G>A
  • NM_130802.3:c.-6G>A
  • NM_130803.3:c.-6G>A
  • NM_130804.3:c.-6G>A
  • LRG_509t2:c.-6G>A
  • LRG_509:g.6180G>A
  • NC_000011.9:g.64577587C>T
  • NM_130799.2:c.-6G>A
Links:
dbSNP: rs768088337
NCBI 1000 Genomes Browser:
rs768088337
Molecular consequence:
  • NM_000244.4:c.-6G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001370251.2:c.-6G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001370259.2:c.-6G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001370260.2:c.-6G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001370261.2:c.-6G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001370262.2:c.-6G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001370263.2:c.-6G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_130799.3:c.-6G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_130800.3:c.-6G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_130801.3:c.-6G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_130802.3:c.-6G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_130803.3:c.-6G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_130804.3:c.-6G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]

Condition(s)

Synonyms:
AllHighlyPenetrant
Identifiers:
MedGen: CN169374

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV002065657Genetic Services Laboratory,University of Chicagocriteria provided, single submitter
Likely benign
(Oct 11, 2021)
germlineclinical testing

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

SCV002074218Women's Health and Genetics/Laboratory Corporation of America, LabCorpcriteria provided, single submitter
Benign
(Jan 11, 2022)
germlineclinical testing

PubMed (2)
[See all records that cite these PMIDs]

Citation Link

Summary from all submissions

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

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

Germline mutation landscape of multiple endocrine neoplasia type 1 using full gene next-generation sequencing.

Carvalho RA, Urtremari B, Jorge AAL, Santana LS, Quedas EPS, Sekiya T, Longuini VC, Montenegro FLM, Lerario AM, Toledo SPA, Marx SJ, Toledo RA, Lourenço DM Jr.

Eur J Endocrinol. 2018 Dec 1;179(6):391-407. doi: 10.1530/EJE-18-0430.

PubMed [citation]
PMID:
30324798
See all PubMed Citations (3)

Details of each submission

From Genetic Services Laboratory,University of Chicago, SCV002065657.1

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

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV002074218.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (2)

Description

Variant summary: MEN1 c.-6G>A is located in the untranslated mRNA region upstream of the initiation codon. The variant allele was found at a frequency of 0.00016 in 136404 control chromosomes (gnomAD). The observed variant frequency is approximately 8-fold of the estimated maximal expected allele frequency for a pathogenic variant in MEN1 causing Multiple Endocrine Neoplasia Type 1 phenotype (2.1e-05), strongly suggesting that the variant is benign. c.-6G>A has been reported in the literature in individuals affected with Multiple Endocrine Neoplasia Type 1 (Carvalho_2018, Damjanovic_2020). These reports do not provide unequivocal conclusions about association of the variant with Multiple Endocrine Neoplasia Type 1. A co-occurrence with a pathogenic variant has been reported (MEN1 c.628_631delACAG, p.Thr210SerfsX13; UMD), providing supporting evidence for a benign role. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. A ClinVar submitter (evaluation after 2014) cites the variant as likely benign while another ClinVar submitter (evaluation after 2014) cites it as uncertain significance. Based on the evidence outlined above, the variant was classified as benign.

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

Last Updated: Nov 29, 2022

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