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NM_020975.4(RET):c.1946C>T (p.Ser649Leu)

Variation ID: Help
24928
Review status: Help
criteria provided, conflicting interpretations1 star out of maximum of 4 stars

Interpretation Help

Allele(s) Help

NM_020975.4(RET):c.1946C>T (p.Ser649Leu)

Allele ID:
36269
Variant type:
single nucleotide variant
Cytogenetic location:
10q11.2
Genomic location:
  • Chr10: 43114546 (on Assembly GRCh38)
  • Chr10: 43609994 (on Assembly GRCh37)
Protein change:
S649L
HGVS:
  • NG_007489.1:g.42478C>T
  • NM_020630.5:c.1946C>T
  • NM_020975.5:c.1946C>T
  • NP_065681.1:p.Ser649Leu
  • NP_066124.1:p.Ser649Leu
  • NC_000010.11:g.43114546C>T (GRCh38)
  • LRG_518t1:c.1946C>T
  • LRG_518t2:c.1946C>T
  • NC_000010.10:g.43609994C>T (GRCh37)
  • NM_020630.4:c.1946C>T
  • NM_020975.4:c.1946C>T
  • LRG_518p1:p.Ser649Leu
  • LRG_518p2:p.Ser649Leu
  • LRG_518:g.42478C>T
Links:
NCBI 1000 Genomes Browser:
rs148935214
Molecular consequence:
NM_020975.5:c.1946C>T: missense variant [Sequence Ontology SO:0001583]
Allele frequency:
  • 1000 Genomes Project 0.00040 (T)
  • 1000 Genomes Project 0.00040
  • Exome Aggregation Consortium (ExAC) 0.00032
  • NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00054
  • The Genome Aggregation Database (gnomAD) 0.00042
  • The Genome Aggregation Database (gnomAD), exomes 0.00032
  • Trans-Omics for Precision Medicine (TOPMed) 0.00044

Assertions for related alleles

NM_020975.4:c.[1902C>G];[1946C>T]

Clinical significance:
Pathogenic
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Number of submission(s):
1
Condition(s)
See supporting ClinVar records

NM_020975.4:c.[1900T>C];[1946C>T]

Clinical significance:
Pathogenic
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Number of submission(s):
1
Condition(s)
See supporting ClinVar records

NM_020975.4(RET):c.1946C>T(;)2372A>T

Clinical significance:
Uncertain significance
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Number of submission(s):
1
See supporting ClinVar records

Variant frequency in dbGaP Help

No dbGaP data has been submitted for this variant.

Browser views

Assertion and evidence details

Germline

Clinical significance
(Last evaluated)
Review status
(Assertion method)
Collection methodCondition(s)
(Mode of inheritance)
OriginCitationsSubmitter - Study nameSubmission accession
Uncertain significance
(Nov 20, 2017)
criteria provided, single submitter
clinical testing
  • Hereditary cancer-predisposing syndrome[MedGen]
germlineAmbry GeneticsSCV000213915.4
Benign
(May 6, 2016)
criteria provided, single submitter
clinical testinggermline
    Center for Pediatric Genomic Medicine,Children's Mercy Hospital and ClinicsSCV000281200.1
    Likely benign
    (Jan 26, 2016)
    criteria provided, single submitter
    clinical testinggermline
      GeneDxSCV000514408.4
      Uncertain significance
      (Jan 24, 2017)
      criteria provided, single submitter
      clinical testinggermline
        Laboratory for Molecular Medicine,Partners HealthCare Personalized MedicineSCV000540172.1
        Likely benign
        (May 16, 2018)
        criteria provided, single submitter
        clinical testingunknownCounsylSCV000786504.2
        Likely benign
        (May 4, 2017)
        criteria provided, single submitter
        clinical testinggermline
          PreventionGenetics,PreventionGeneticsSCV000807017.1
          Uncertain significance
          (Aug 1, 2018)
          criteria provided, single submitter
          clinical testing
          • Hereditary cancer-predisposing syndrome[MedGen]
          germline
            GeneKor MSASCV000822193.1
            Uncertain significance
            (Jul 2, 2018)
            criteria provided, single submitter
            clinical testingunknown
              Mendelics Analise GenomicaSCV000838393.1
              Likely benign
              (Dec 20, 2017)
              criteria provided, single submitter
              clinical testinggermline
                InvitaeSCV000166611.7
                Likely benign
                (Jun 1, 2014)
                no assertion criteria providedresearch
                • Elevated basal serum calcitonin (Autosomal dominant inheritance)[MedGen]
                germline
                  CSER_CC_NCGL; University of Washington Medical Center - ESP 6500 variant annotation
                  Study description
                  SCV000190507.1
                  Uncertain significance
                  (May 4, 2018)
                  no assertion criteria providedliterature onlygermlineARUP Institute,ARUP LaboratoriesSCV000055379.2
                  not provided
                  (Sep 19, 2013)
                  no assertion providedreference populationgermlineITMISCV000086187.1
                  SubmitterFamiliesIndividualsAllele originEthnicityGeographic originCitations and DatabasesDescription
                  Total for all submittersnot provided1germline, unknown
                  African; African_European; Central_Asian; East_Asian; European; Hispanic; Whole_cohort
                  not provided
                  ARUP Institute,ARUP Laboratoriesnot providednot providedgermlinenot providednot providedPMID 19906784 and 29656518 ind…Full description
                  Ambry Geneticsnot provided1germlinenot providednot providedLines of evidence used in supp…Full description
                  CSER_CC_NCGL; University of Washington Medical Centernot providednot providedgermlinenot providednot providednot providednot provided
                  Center for Pediatric Genomic Medicine,Children's Mercy Hospital and Clinicsnot providednot providedgermlinenot providednot providednot providednot provided
                  Counsylnot providednot providedunknownnot providednot providednot provided
                  GeneDxnot providednot providedgermlinenot providednot providednot providedThis variant is considered lik…Full description
                  GeneKor MSAnot providednot providedgermlinenot providednot providednot providednot provided
                  ITMInot providednot providedgermline
                  African; African_European; Central_Asian; East_Asian; European; Hispanic; Whole_cohort
                  not providednot providednot provided
                  Invitaenot providednot providedgermlinenot providednot providednot providednot provided
                  Laboratory for Molecular Medicine,Partners HealthCare Personalized Medicinenot providednot providedgermlinenot providednot providednot providedVariant identified in a genome…Full description
                  Mendelics Analise Genomicanot providednot providedunknownnot providednot providednot providednot provided
                  PreventionGenetics,PreventionGeneticsnot providednot providedgermlinenot providednot providednot providednot provided
                  SubmitterAllele originIndividualsPhenotypes (Affected status)EthnicityGeographic originCitationsDescription

                  Last Updated: Feb 11, 2019

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