NM_020975.6(RET):c.375C>A (p.Val125=) AND not specified
- Germline classification:
- Benign (8 submissions)
- Last evaluated:
- Aug 15, 2023
- Review status:
- 2 stars out of maximum of 4 starscriteria provided, multiple submitters, no conflicts
- Somatic classification
of clinical impact: - None
- Review status:
- (0/4) 0 stars out of maximum of 4 starsno assertion criteria provided
- Somatic classification
of oncogenicity: - None
- Review status:
- (0/4) 0 stars out of maximum of 4 starsno assertion criteria provided
- Record status:
- current
- Accession:
- RCV000082057.32
Allele description [Variation Report for NM_020975.6(RET):c.375C>A (p.Val125=)]
NM_020975.6(RET):c.375C>A (p.Val125=)
- 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.375C>A (p.Val125=)
- HGVS:
- NC_000010.11:g.43102379C>A
- NG_007489.1:g.30311C>A
- NM_000323.2:c.375C>A
- NM_001406743.1:c.375C>A
- NM_001406744.1:c.375C>A
- NM_001406759.1:c.375C>A
- NM_001406760.1:c.375C>A
- NM_001406761.1:c.338-92C>A
- NM_001406762.1:c.338-92C>A
- NM_001406763.1:c.375C>A
- NM_001406764.1:c.338-92C>A
- NM_001406765.1:c.375C>A
- NM_001406766.1:c.337+1657C>A
- NM_001406767.1:c.337+1657C>A
- NM_001406768.1:c.338-92C>A
- NM_001406769.1:c.375C>A
- NM_001406770.1:c.337+1657C>A
- NM_001406771.1:c.375C>A
- NM_001406772.1:c.375C>A
- NM_001406773.1:c.375C>A
- NM_001406774.1:c.338-92C>A
- NM_001406775.1:c.337+1657C>A
- NM_001406776.1:c.337+1657C>A
- NM_001406777.1:c.337+1657C>A
- NM_001406778.1:c.337+1657C>A
- NM_001406779.1:c.375C>A
- NM_001406780.1:c.375C>A
- NM_001406781.1:c.375C>A
- NM_001406782.1:c.375C>A
- NM_001406783.1:c.338-92C>A
- NM_001406784.1:c.74-6652C>A
- NM_001406785.1:c.375C>A
- NM_001406786.1:c.338-92C>A
- NM_001406787.1:c.375C>A
- NM_001406788.1:c.337+1657C>A
- NM_001406789.1:c.337+1657C>A
- NM_001406790.1:c.337+1657C>A
- NM_001406791.1:c.337+1657C>A
- NM_001406792.1:c.74-9720C>A
- NM_001406793.1:c.74-9720C>A
- NM_001406794.1:c.74-9720C>A
- NM_020629.2:c.375C>A
- NM_020630.7:c.375C>A
- NM_020975.6:c.375C>AMANE SELECT
- NP_000314.1:p.Val125=
- NP_001393672.1:p.Val125=
- NP_001393673.1:p.Val125=
- NP_001393688.1:p.Val125=
- NP_001393689.1:p.Val125=
- NP_001393692.1:p.Val125=
- NP_001393694.1:p.Val125=
- NP_001393698.1:p.Val125=
- NP_001393700.1:p.Val125=
- NP_001393701.1:p.Val125=
- NP_001393702.1:p.Val125=
- NP_001393708.1:p.Val125=
- NP_001393709.1:p.Val125=
- NP_001393710.1:p.Val125=
- NP_001393711.1:p.Val125=
- NP_001393714.1:p.Val125=
- NP_001393716.1:p.Val125=
- NP_065680.1:p.Val125=
- NP_065681.1:p.Val125=
- NP_065681.1:p.Val125=
- NP_066124.1:p.Val125=
- NP_066124.1:p.Val125=
- LRG_518t1:c.375C>A
- LRG_518t2:c.375C>A
- LRG_518:g.30311C>A
- LRG_518p1:p.Val125=
- LRG_518p2:p.Val125=
- NC_000010.10:g.43597827C>A
- NM_020630.4:c.375C>A
- NM_020975.4:c.375C>A
- NP_066124.1:p.(=)
- p.V125V
- p.Val125Val
This HGVS expression did not pass validation- Links:
- dbSNP: rs1800859
- NCBI 1000 Genomes Browser:
- rs1800859
- Molecular consequence:
- NM_001406761.1:c.338-92C>A - intron variant - [Sequence Ontology: SO:0001627]
- NM_001406762.1:c.338-92C>A - intron variant - [Sequence Ontology: SO:0001627]
- NM_001406764.1:c.338-92C>A - intron variant - [Sequence Ontology: SO:0001627]
- NM_001406766.1:c.337+1657C>A - intron variant - [Sequence Ontology: SO:0001627]
- NM_001406767.1:c.337+1657C>A - intron variant - [Sequence Ontology: SO:0001627]
- NM_001406768.1:c.338-92C>A - intron variant - [Sequence Ontology: SO:0001627]
- NM_001406770.1:c.337+1657C>A - intron variant - [Sequence Ontology: SO:0001627]
- NM_001406774.1:c.338-92C>A - intron variant - [Sequence Ontology: SO:0001627]
- NM_001406775.1:c.337+1657C>A - intron variant - [Sequence Ontology: SO:0001627]
- NM_001406776.1:c.337+1657C>A - intron variant - [Sequence Ontology: SO:0001627]
- NM_001406777.1:c.337+1657C>A - intron variant - [Sequence Ontology: SO:0001627]
- NM_001406778.1:c.337+1657C>A - intron variant - [Sequence Ontology: SO:0001627]
- NM_001406783.1:c.338-92C>A - intron variant - [Sequence Ontology: SO:0001627]
- NM_001406784.1:c.74-6652C>A - intron variant - [Sequence Ontology: SO:0001627]
- NM_001406786.1:c.338-92C>A - intron variant - [Sequence Ontology: SO:0001627]
- NM_001406788.1:c.337+1657C>A - intron variant - [Sequence Ontology: SO:0001627]
- NM_001406789.1:c.337+1657C>A - intron variant - [Sequence Ontology: SO:0001627]
- NM_001406790.1:c.337+1657C>A - intron variant - [Sequence Ontology: SO:0001627]
- NM_001406791.1:c.337+1657C>A - intron variant - [Sequence Ontology: SO:0001627]
- NM_001406792.1:c.74-9720C>A - intron variant - [Sequence Ontology: SO:0001627]
- NM_001406793.1:c.74-9720C>A - intron variant - [Sequence Ontology: SO:0001627]
- NM_001406794.1:c.74-9720C>A - intron variant - [Sequence Ontology: SO:0001627]
- NM_000323.2:c.375C>A - synonymous variant - [Sequence Ontology: SO:0001819]
- NM_001406743.1:c.375C>A - synonymous variant - [Sequence Ontology: SO:0001819]
- NM_001406744.1:c.375C>A - synonymous variant - [Sequence Ontology: SO:0001819]
- NM_001406759.1:c.375C>A - synonymous variant - [Sequence Ontology: SO:0001819]
- NM_001406760.1:c.375C>A - synonymous variant - [Sequence Ontology: SO:0001819]
- NM_001406763.1:c.375C>A - synonymous variant - [Sequence Ontology: SO:0001819]
- NM_001406765.1:c.375C>A - synonymous variant - [Sequence Ontology: SO:0001819]
- NM_001406769.1:c.375C>A - synonymous variant - [Sequence Ontology: SO:0001819]
- NM_001406771.1:c.375C>A - synonymous variant - [Sequence Ontology: SO:0001819]
- NM_001406772.1:c.375C>A - synonymous variant - [Sequence Ontology: SO:0001819]
- NM_001406773.1:c.375C>A - synonymous variant - [Sequence Ontology: SO:0001819]
- NM_001406779.1:c.375C>A - synonymous variant - [Sequence Ontology: SO:0001819]
- NM_001406780.1:c.375C>A - synonymous variant - [Sequence Ontology: SO:0001819]
- NM_001406781.1:c.375C>A - synonymous variant - [Sequence Ontology: SO:0001819]
- NM_001406782.1:c.375C>A - synonymous variant - [Sequence Ontology: SO:0001819]
- NM_001406785.1:c.375C>A - synonymous variant - [Sequence Ontology: SO:0001819]
- NM_001406787.1:c.375C>A - synonymous variant - [Sequence Ontology: SO:0001819]
- NM_020629.2:c.375C>A - synonymous variant - [Sequence Ontology: SO:0001819]
- NM_020630.7:c.375C>A - synonymous variant - [Sequence Ontology: SO:0001819]
- NM_020975.6:c.375C>A - synonymous variant - [Sequence Ontology: SO:0001819]
- Observations:
- 1
Condition(s)
- Synonyms:
- AllHighlyPenetrant
- Identifiers:
- MedGen: CN169374
-
Taxonomy Links for Nucleotide (Select 2691527841) (0)
Taxonomy
-
Protein Links for Nucleotide (Select 1852366096) (174)
Protein
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See more...Assertion and evidence details
Submission Accession | Submitter | Review Status (Assertion method) | Clinical Significance (Last evaluated) | Origin | Method | Citations |
---|---|---|---|---|---|---|
SCV000113996 | Eurofins Ntd Llc (ga) | criteria provided, single submitter (EGL Classification Definitions 2015) | Benign (Aug 20, 2012) | germline | clinical testing | |
SCV000313728 | PreventionGenetics, part of Exact Sciences | criteria provided, single submitter (ACMG Guidelines, 2015) | Benign | germline | clinical testing | |
SCV000514407 | GeneDx | criteria provided, single submitter (GeneDx Variant Classification (06012015)) | Benign (May 8, 2015) | germline | clinical testing | |
SCV000967108 | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | criteria provided, single submitter (LMM Criteria) | Benign (Feb 21, 2013) | germline | clinical testing | |
SCV001742013 | Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen - VKGL Data-share Consensus | no assertion criteria provided | Benign | germline | clinical testing | |
SCV001808562 | Genome Diagnostics Laboratory, Amsterdam University Medical Center - VKGL Data-share Consensus | no assertion criteria provided | Benign | germline | clinical testing | |
SCV001956008 | Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ - VKGL Data-share Consensus
| no assertion criteria provided | Benign | germline | clinical testing | |
SCV002760461 | Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital | criteria provided, single submitter (ACMG Guidelines, 2015) | Benign (Aug 15, 2023) | germline | clinical testing |
Summary from all submissions
Ethnicity | Origin | Affected | Individuals | Families | Chromosomes tested | Number Tested | Family history | Method |
---|---|---|---|---|---|---|---|---|
not provided | germline | yes | not provided | not provided | not provided | not provided | not provided | clinical testing |
not provided | germline | not provided | 1 | 1 | not provided | not provided | not provided | clinical testing |
not provided | germline | unknown | 2 | not provided | not provided | not provided | not provided | clinical 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.
- PMID:
- 24033266
- PMCID:
- PMC3995020
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.
- PMID:
- 25741868
- PMCID:
- PMC4544753
Details of each submission
From Eurofins Ntd Llc (ga), SCV000113996.8
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | 2 | not provided | not provided | clinical testing | 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 | 2 | not provided | not provided | not provided |
From PreventionGenetics, part of Exact Sciences, SCV000313728.1
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | clinical testing | PubMed (1) |
# | 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 GeneDx, SCV000514407.4
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | clinical testing | not 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.
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | germline | yes | not provided | not provided | not provided | not provided | not provided | not provided | not provided |
From Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, SCV000967108.1
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | 1 | not provided | not provided | clinical testing | PubMed (1) |
Description
Val125Val in exon 3 of RET: 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. It has been identified in 1.2% (102/8600) of Eur opean American chromosomes from a broad population by the NHLBI Exome Sequencing Project (http://evs.gs.washington.edu/EVS; dbSNP rs1800859).
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | germline | not provided | not provided | not provided | not provided | 1 | not provided | 1 | not provided |
From Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen - VKGL Data-share Consensus, SCV001742013.3
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | clinical testing | not provided |
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | germline | yes | not provided | not provided | not provided | not provided | not provided | not provided | not provided |
From Genome Diagnostics Laboratory, Amsterdam University Medical Center - VKGL Data-share Consensus, SCV001808562.1
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | clinical testing | not provided |
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | germline | yes | not provided | not provided | not provided | not provided | not provided | not provided | not provided |
From Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ - VKGL Data-share Consensus, SCV001956008.1
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | clinical testing | not provided |
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | germline | yes | not provided | not provided | not provided | not provided | not provided | not provided | not provided |
From Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital, SCV002760461.3
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | clinical testing | PubMed (1) |
# | 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: Jun 9, 2024