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NM_006393.3(NEBL):c.120A>G (p.Glu40=) AND not specified

Germline classification:
Benign/Likely benign (4 submissions)
Last evaluated:
Aug 19, 2023
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:
RCV000038683.9

Allele description [Variation Report for NM_006393.3(NEBL):c.120A>G (p.Glu40=)]

NM_006393.3(NEBL):c.120A>G (p.Glu40=)

Gene:
NEBL:nebulette [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
10p12.31
Genomic location:
Preferred name:
NM_006393.3(NEBL):c.120A>G (p.Glu40=)
HGVS:
  • NC_000010.11:g.20896991T>C
  • NG_017092.1:g.282197A>G
  • NM_001173484.2:c.357+64681A>G
  • NM_001377322.1:c.357+64681A>G
  • NM_001377323.1:c.309+64681A>G
  • NM_001377324.1:c.300+64681A>G
  • NM_001377325.1:c.291+64681A>G
  • NM_001377326.1:c.249+64681A>G
  • NM_001377327.1:c.249+64681A>G
  • NM_001377328.1:c.249+64681A>G
  • NM_006393.3:c.120A>GMANE SELECT
  • NM_213569.2:c.357+64681A>G
  • NP_006384.1:p.Glu40=
  • NP_006384.1:p.Glu40=
  • LRG_411t1:c.357+64681A>G
  • LRG_411t2:c.120A>G
  • LRG_411:g.282197A>G
  • LRG_411p2:p.Glu40=
  • NC_000010.10:g.21185920T>C
  • NM_006393.2:c.120A>G
  • c.120A>G
  • p.Glu40Glu
Links:
dbSNP: rs397517203
NCBI 1000 Genomes Browser:
rs397517203
Molecular consequence:
  • NM_001173484.2:c.357+64681A>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001377322.1:c.357+64681A>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001377323.1:c.309+64681A>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001377324.1:c.300+64681A>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001377325.1:c.291+64681A>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001377326.1:c.249+64681A>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001377327.1:c.249+64681A>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001377328.1:c.249+64681A>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_213569.2:c.357+64681A>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_006393.3:c.120A>G - synonymous variant - [Sequence Ontology: SO:0001819]
Observations:
1

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
SCV000062361Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine
criteria provided, single submitter

(LMM Criteria)
Likely benign
(Sep 24, 2012)
germlineclinical testing

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

SCV000728575GeneDx
criteria provided, single submitter

(GeneDx Variant Classification (06012015))
Benign
(Sep 24, 2015)
germlineclinical testing

Citation Link,

SCV002651970Ambry Genetics
criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)
Likely benign
(Jun 12, 2022)
germlineclinical testing

Citation Link,

SCV004038154Women's Health and Genetics/Laboratory Corporation of America, LabCorp
criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)
Benign
(Aug 19, 2023)
germlineclinical testing

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlinenot provided11not providednot providednot providedclinical testing
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

A systematic approach to assessing the clinical significance of genetic variants.

Duzkale H, Shen J, McLaughlin H, Alfares A, Kelly MA, Pugh TJ, Funke BH, Rehm HL, Lebo MS.

Clin Genet. 2013 Nov;84(5):453-63. doi: 10.1111/cge.12257.

PubMed [citation]
PMID:
24033266
PMCID:
PMC3995020

Details of each submission

From Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, SCV000062361.6

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testing PubMed (1)

Description

Glu40Glu in exon 2 of NEBL: This variant is not expected to have clinical signif icance because it does not alter an amino acid residue and is not located within the splice consensus sequence. Glu40Glu in exon 2 of NEBL (allele frequency = n/a)

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenot providednot providednot providednot provided1not provided1not provided

From GeneDx, SCV000728575.1

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

Description

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.

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

From Ambry Genetics, SCV002651970.2

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

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.

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

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV004038154.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Jul 15, 2024