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NM_020975.6(RET):c.166C>A (p.Leu56Met) AND not specified

Germline classification:
Benign/Likely benign (8 submissions)
Last evaluated:
Jul 31, 2024
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:
RCV000121985.42

Allele description [Variation Report for NM_020975.6(RET):c.166C>A (p.Leu56Met)]

NM_020975.6(RET):c.166C>A (p.Leu56Met)

Gene:
RET:ret proto-oncogene [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
10q11.21
Genomic location:
Preferred name:
NM_020975.6(RET):c.166C>A (p.Leu56Met)
HGVS:
  • NC_000010.11:g.43100551C>A
  • NG_007489.1:g.28483C>A
  • NM_000323.2:c.166C>A
  • NM_001406743.1:c.166C>A
  • NM_001406744.1:c.166C>A
  • NM_001406759.1:c.166C>A
  • NM_001406760.1:c.166C>A
  • NM_001406761.1:c.166C>A
  • NM_001406762.1:c.166C>A
  • NM_001406763.1:c.166C>A
  • NM_001406764.1:c.166C>A
  • NM_001406765.1:c.166C>A
  • NM_001406766.1:c.166C>A
  • NM_001406767.1:c.166C>A
  • NM_001406768.1:c.166C>A
  • NM_001406769.1:c.166C>A
  • NM_001406770.1:c.166C>A
  • NM_001406771.1:c.166C>A
  • NM_001406772.1:c.166C>A
  • NM_001406773.1:c.166C>A
  • NM_001406774.1:c.166C>A
  • NM_001406775.1:c.166C>A
  • NM_001406776.1:c.166C>A
  • NM_001406777.1:c.166C>A
  • NM_001406778.1:c.166C>A
  • NM_001406779.1:c.166C>A
  • NM_001406780.1:c.166C>A
  • NM_001406781.1:c.166C>A
  • NM_001406782.1:c.166C>A
  • NM_001406783.1:c.166C>A
  • NM_001406785.1:c.166C>A
  • NM_001406786.1:c.166C>A
  • NM_001406787.1:c.166C>A
  • NM_001406788.1:c.166C>A
  • NM_001406789.1:c.166C>A
  • NM_001406790.1:c.166C>A
  • NM_001406791.1:c.166C>A
  • NM_020629.2:c.166C>A
  • NM_020630.7:c.166C>A
  • NM_020975.6:c.166C>AMANE SELECT
  • NP_000314.1:p.Leu56Met
  • NP_001393672.1:p.Leu56Met
  • NP_001393673.1:p.Leu56Met
  • NP_001393688.1:p.Leu56Met
  • NP_001393689.1:p.Leu56Met
  • NP_001393690.1:p.Leu56Met
  • NP_001393691.1:p.Leu56Met
  • NP_001393692.1:p.Leu56Met
  • NP_001393693.1:p.Leu56Met
  • NP_001393694.1:p.Leu56Met
  • NP_001393695.1:p.Leu56Met
  • NP_001393696.1:p.Leu56Met
  • NP_001393697.1:p.Leu56Met
  • NP_001393698.1:p.Leu56Met
  • NP_001393699.1:p.Leu56Met
  • NP_001393700.1:p.Leu56Met
  • NP_001393701.1:p.Leu56Met
  • NP_001393702.1:p.Leu56Met
  • NP_001393703.1:p.Leu56Met
  • NP_001393704.1:p.Leu56Met
  • NP_001393705.1:p.Leu56Met
  • NP_001393706.1:p.Leu56Met
  • NP_001393707.1:p.Leu56Met
  • NP_001393708.1:p.Leu56Met
  • NP_001393709.1:p.Leu56Met
  • NP_001393710.1:p.Leu56Met
  • NP_001393711.1:p.Leu56Met
  • NP_001393712.1:p.Leu56Met
  • NP_001393714.1:p.Leu56Met
  • NP_001393715.1:p.Leu56Met
  • NP_001393716.1:p.Leu56Met
  • NP_001393717.1:p.Leu56Met
  • NP_001393718.1:p.Leu56Met
  • NP_001393719.1:p.Leu56Met
  • NP_001393720.1:p.Leu56Met
  • NP_065680.1:p.Leu56Met
  • NP_065681.1:p.Leu56Met
  • NP_065681.1:p.Leu56Met
  • NP_065681.1:p.Leu56Met
  • NP_066124.1:p.Leu56Met
  • NP_066124.1:p.Leu56Met
  • LRG_518t1:c.166C>A
  • LRG_518t2:c.166C>A
  • LRG_518:g.28483C>A
  • LRG_518p1:p.Leu56Met
  • LRG_518p2:p.Leu56Met
  • NC_000010.10:g.43595999C>A
  • NM_020630.4:c.166C>A
  • NM_020630.6:c.166C>A
  • NM_020975.4:c.166C>A
  • NM_020975.4:c.166C>A
  • NM_020975.5:c.166C>A
  • p.L56M
Protein change:
L56M
Links:
dbSNP: rs145633958
NCBI 1000 Genomes Browser:
rs145633958
Molecular consequence:
  • NM_000323.2:c.166C>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406743.1:c.166C>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406744.1:c.166C>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406759.1:c.166C>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406760.1:c.166C>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406761.1:c.166C>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406762.1:c.166C>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406763.1:c.166C>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406764.1:c.166C>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406765.1:c.166C>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406766.1:c.166C>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406767.1:c.166C>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406768.1:c.166C>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406769.1:c.166C>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406770.1:c.166C>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406771.1:c.166C>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406772.1:c.166C>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406773.1:c.166C>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406774.1:c.166C>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406775.1:c.166C>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406776.1:c.166C>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406777.1:c.166C>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406778.1:c.166C>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406779.1:c.166C>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406780.1:c.166C>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406781.1:c.166C>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406782.1:c.166C>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406783.1:c.166C>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406785.1:c.166C>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406786.1:c.166C>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406787.1:c.166C>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406788.1:c.166C>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406789.1:c.166C>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406790.1:c.166C>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406791.1:c.166C>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_020629.2:c.166C>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_020630.7:c.166C>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_020975.6:c.166C>A - missense variant - [Sequence Ontology: SO:0001583]
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
SCV000086196ITMI
no classification provided
not providedgermlinereference population

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

SCV000113984Eurofins Ntd Llc (ga)
criteria provided, single submitter

(EGL Classification Definitions 2015)
Benign
(Jun 19, 2014)
germlineclinical testing

Citation Link,

SCV000711342Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine
criteria provided, single submitter

(LMM Criteria)
Likely benign
(Apr 20, 2016)
germlineclinical testing

PubMed (6)
[See all records that cite these PMIDs]

SCV000807009PreventionGenetics, part of Exact Sciences
criteria provided, single submitter

(ACMG Guidelines, 2015)
Benign
(Oct 10, 2016)
germlineclinical testing

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

SCV001807872Genome Diagnostics Laboratory, Amsterdam University Medical Center - VKGL Data-share Consensus
no assertion criteria provided
Benigngermlineclinical testing

SCV001952151Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ - VKGL Data-share Consensus

See additional submitters

no assertion criteria provided
Benigngermlineclinical testing

SCV002067079Genetic Services Laboratory, University of Chicago
criteria provided, single submitter

(ACMG Guidelines, 2015)
Benign
(Aug 17, 2020)
germlineclinical testing

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

SCV002550377Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital
criteria provided, single submitter

(ACMG Guidelines, 2015)
Likely benign
(Jul 31, 2024)
germlineclinical testing

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknown3not providednot providednot providednot providedclinical testing
not providedgermlinenot provided11not providednot providednot providedclinical testing
not providedgermlinenonot providednot providednot providednot providednot providedclinical testing
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing
Africangermlineunknownnot providednot providednot provided43not providedreference population
African_Europeangermlineunknownnot providednot providednot provided46not providedreference population
Central_Asiangermlineunknownnot providednot providednot provided50not providedreference population
East_Asiangermlineunknownnot providednot providednot provided62not providedreference population
Europeangermlineunknownnot providednot providednot provided331not providedreference population
Hispanicgermlineunknownnot providednot providednot provided118not providedreference population
Whole_cohortgermlineunknownnot providednot providednot provided681not providedreference population

Citations

PubMed

Germline variation in cancer-susceptibility genes in a healthy, ancestrally diverse cohort: implications for individual genome sequencing.

Bodian DL, McCutcheon JN, Kothiyal P, Huddleston KC, Iyer RK, Vockley JG, Niederhuber JE.

PLoS One. 2014;9(4):e94554. doi: 10.1371/journal.pone.0094554.

PubMed [citation]
PMID:
24728327
PMCID:
PMC3984285

Hirschsprung's disease and variants in genes that regulate enteric neural crest cell proliferation, migration and differentiation.

Carter TC, Kay DM, Browne ML, Liu A, Romitti PA, Kuehn D, Conley MR, Caggana M, Druschel CM, Brody LC, Mills JL.

J Hum Genet. 2012 Aug;57(8):485-93. doi: 10.1038/jhg.2012.54. Epub 2012 May 31.

PubMed [citation]
PMID:
22648184
PMCID:
PMC3503526
See all PubMed Citations (8)

Details of each submission

From ITMI, SCV000086196.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1Africannot providednot providednot providedreference population PubMed (1)
2African_Europeannot providednot providednot providedreference population PubMed (1)
3Central_Asiannot providednot providednot providedreference population PubMed (1)
4East_Asiannot providednot providednot providedreference population PubMed (1)
5Europeannot providednot providednot providedreference population PubMed (1)
6Hispanicnot providednot providednot providedreference population PubMed (1)
7Whole_cohortnot providednot providednot providedreference population PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknown43not provideddiscoverynot provided0not providednot provided
2germlineunknown46not provideddiscoverynot provided0not providednot provided
3germlineunknown50not provideddiscoverynot provided0not providednot provided
4germlineunknown62not provideddiscoverynot provided0not providednot provided
5germlineunknown331not provideddiscoverynot provided0.0076not providednot provided
6germlineunknown118not provideddiscoverynot provided0.0042not providednot provided
7germlineunknown681not provideddiscoverynot provided0.0044not providednot provided

From Eurofins Ntd Llc (ga), SCV000113984.8

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided3not providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot provided3not providednot providednot provided

From Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, SCV000711342.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testing PubMed (6)

Description

p.Leu56Met in exon 2 of RET: This variant is not expected to have clinical signi ficance because it has been identified in 0.4% (271/66206) of European chromosom es, including 1 homozygote by the Exome Aggregation Consortium (ExAC, http://exa c.broadinstitute.org; dbSNP rs145633958).

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

From PreventionGenetics, part of Exact Sciences, SCV000807009.1

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

From Genome Diagnostics Laboratory, Amsterdam University Medical Center - VKGL Data-share Consensus, SCV001807872.1

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

From Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ - VKGL Data-share Consensus, SCV001952151.1

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

From Genetic Services Laboratory, University of Chicago, SCV002067079.1

#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 Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital, SCV002550377.6

#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: Nov 3, 2024