NM_003001.5(SDHC):c.180-9T>C AND multiple conditions

Germline classification:: Likely benign (1 submission)
Last evaluated:: Aug 23, 2022
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

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:: RCV001411905.9

Allele description [Variation Report for NM_003001.5(SDHC):c.180-9T>C]

NM_003001.5(SDHC):c.180-9T>C

Gene:

SDHC:succinate dehydrogenase complex subunit C [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

1q23.3

Genomic location:

Preferred name:

NM_003001.5(SDHC):c.180-9T>C

HGVS:

NC_000001.11:g.161340585T>C
NG_012767.1:g.31210T>C
NM_001035511.3:c.180-9T>C
NM_001035512.3:c.78-9T>C
NM_001035513.3:c.21-9T>C
NM_001278172.3:c.78-9T>C
NM_001407115.1:c.300-9T>C
NM_001407116.1:c.123-9T>C
NM_001407117.1:c.123-9T>C
NM_001407118.1:c.78-9T>C
NM_001407119.1:c.69-9T>C
NM_001407120.1:c.69-9T>C
NM_001407121.1:c.123-9T>C
NM_003001.5:c.180-9T>CMANE SELECT
LRG_317:g.31210T>C
NC_000001.10:g.161310375T>C

Links:

dbSNP: rs2102335976

NCBI 1000 Genomes Browser:

rs2102335976

Molecular consequence:

NM_001035511.3:c.180-9T>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001035512.3:c.78-9T>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001035513.3:c.21-9T>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001278172.3:c.78-9T>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001407115.1:c.300-9T>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001407116.1:c.123-9T>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001407117.1:c.123-9T>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001407118.1:c.78-9T>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001407119.1:c.69-9T>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001407120.1:c.69-9T>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001407121.1:c.123-9T>C - intron variant - [Sequence Ontology: SO:0001627]
NM_003001.5:c.180-9T>C - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Name:: Gastrointestinal stromal tumor
Synonyms:: Gastrointestinal Stromal Sarcoma; Gastrointestinal stromal tumor, somatic; Gastrointestinal stroma tumor
Identifiers:: MONDO: MONDO:0011719; MeSH: D046152; MedGen: C0238198; Orphanet: 44890; OMIM: 606764; Human Phenotype Ontology: HP:0100723

Name:: Paragangliomas 3 (PPGL3)
Synonyms:: Glomus tumors, familial, 3; SDHC-Related Hereditary Paraganglioma-Pheochromocytoma Syndrome (Paragangliomas 3); PHEOCHROMOCYTOMA/PARAGANGLIOMA SYNDROME 3
Identifiers:: MONDO: MONDO:0011544; MedGen: C1854336; Orphanet: 29072; OMIM: 605373

Recent activity

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PREDICTED: Homo sapiens multiple inositol-polyphosphate phosphatase 1 (MINPP1), ...
PREDICTED: Homo sapiens multiple inositol-polyphosphate phosphatase 1 (MINPP1), transcript variant X1, mRNA
gi|2462522002|ref|XM_054367221.1|

Nucleotide
Pathogen: clinical or host-associated sample from Streptococcus agalactiae
Pathogen: clinical or host-associated sample from Streptococcus agalactiae

biosample
PREDICTED: Piliocolobus tephrosceles ISG15 ubiquitin like modifier (ISG15), mRNA
PREDICTED: Piliocolobus tephrosceles ISG15 ubiquitin like modifier (ISG15), mRNA
gi|1788669918|ref|XM_023192830.2|

Nucleotide
Streptococcus agalactiae strain SH2515, whole genome shotgun sequencing project
Streptococcus agalactiae strain SH2515, whole genome shotgun sequencing project
gi|825919641|gb|LDAK00000000.1|LDAK 000

Nucleotide
Streptococcus agalactiae strain ES-PW-080, whole genome shotgun sequencing proje...
Streptococcus agalactiae strain ES-PW-080, whole genome shotgun sequencing project
gi|825820233|gb|LCVD00000000.1|LCVD 000

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001613976	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Likely benign (Aug 23, 2022)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001613976

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Likely benign
(Aug 23, 2022)

germline

clinical testing

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

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

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001613976.4

#	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: Sep 29, 2024

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