NM_001370259.2(MEN1):c.655-4del AND Hereditary cancer-predisposing syndrome

Germline classification:: Benign/Likely benign (2 submissions)
Last evaluated:: Dec 7, 2021
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV000566396.5

Allele description [Variation Report for NM_001370259.2(MEN1):c.655-4del]

NM_001370259.2(MEN1):c.655-4del

Gene:

MEN1:menin 1 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

11q13.1

Genomic location:

Preferred name:

NM_001370259.2(MEN1):c.655-4del

HGVS:

NC_000011.10:g.64807684del
NG_008929.1:g.8611del
NG_033040.1:g.558del
NM_000244.4:c.670-4del
NM_001370251.2:c.655-4del
NM_001370259.2:c.655-4delMANE SELECT
NM_001370260.2:c.655-4del
NM_001370261.2:c.655-4del
NM_001370262.2:c.550-4del
NM_001370263.2:c.550-4del
NM_130799.3:c.655-4del
NM_130800.3:c.670-4del
NM_130801.3:c.670-4del
NM_130802.3:c.670-4del
NM_130803.3:c.670-4del
NM_130804.3:c.670-4del
LRG_509t2:c.655-4del
LRG_509:g.8611del
NC_000011.9:g.64575156del
NC_000011.9:g.64575156delA
NM_130799.2:c.655-4del
NM_130799.2:c.655-4delT
NM_130804.2:c.670-4delT

Links:

dbSNP: rs748005956

NCBI 1000 Genomes Browser:

rs748005956

Molecular consequence:

NM_000244.4:c.670-4del - intron variant - [Sequence Ontology: SO:0001627]
NM_001370251.2:c.655-4del - intron variant - [Sequence Ontology: SO:0001627]
NM_001370259.2:c.655-4del - intron variant - [Sequence Ontology: SO:0001627]
NM_001370260.2:c.655-4del - intron variant - [Sequence Ontology: SO:0001627]
NM_001370261.2:c.655-4del - intron variant - [Sequence Ontology: SO:0001627]
NM_001370262.2:c.550-4del - intron variant - [Sequence Ontology: SO:0001627]
NM_001370263.2:c.550-4del - intron variant - [Sequence Ontology: SO:0001627]
NM_130799.3:c.655-4del - intron variant - [Sequence Ontology: SO:0001627]
NM_130800.3:c.670-4del - intron variant - [Sequence Ontology: SO:0001627]
NM_130801.3:c.670-4del - intron variant - [Sequence Ontology: SO:0001627]
NM_130802.3:c.670-4del - intron variant - [Sequence Ontology: SO:0001627]
NM_130803.3:c.670-4del - intron variant - [Sequence Ontology: SO:0001627]
NM_130804.3:c.670-4del - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Name:: Hereditary cancer-predisposing syndrome
Synonyms:: Neoplastic Syndromes, Hereditary; Tumor predisposition; Cancer predisposition; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0015356; MeSH: D009386; MedGen: C0027672

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SPDYE1-AS1 SPDYE1 and UBE2D4 antisense RNA 1 [Homo sapiens]
SPDYE1-AS1 SPDYE1 and UBE2D4 antisense RNA 1 [Homo sapiens]
Gene ID:131554431

Gene

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000673632	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Likely benign (Oct 15, 2019)	germline	clinical testing	PubMed (1) [See all records that cite this PMID] Citation Link,
SCV002530077	Sema4, Sema4	criteria provided, single submitter (Sema4 Curation Guidelines)	Benign (Dec 7, 2021)	germline	curation	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000673632

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Likely benign
(Oct 15, 2019)

germline

clinical testing

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

Citation Link,

SCV002530077

Sema4, Sema4

criteria provided, single submitter

(Sema4 Curation Guidelines)

Benign
(Dec 7, 2021)

germline

curation

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing, curation

Citations

PubMed

MEN1 gene mutation analysis in Italian patients with multiple endocrine neoplasia type 1.

Morelli A, Falchetti A, Martineti V, Becherini L, Mark M, Friedman E, Brandi ML.

Eur J Endocrinol. 2000 Feb;142(2):131-7.

PubMed [citation]

PMID:: 10664520

Details of each submission

From Ambry Genetics, SCV000673632.5

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

Description

This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Sema4, Sema4, SCV002530077.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	curation	not provided

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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