NM_005359.6(SMAD4):c.-3C>G AND Hereditary cancer-predisposing syndrome

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jan 18, 2023
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:: RCV000571774.6

Allele description [Variation Report for NM_005359.6(SMAD4):c.-3C>G]

NM_005359.6(SMAD4):c.-3C>G

Gene:

SMAD4:SMAD family member 4 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

18q21.2

Genomic location:

Preferred name:

NM_005359.6(SMAD4):c.-3C>G

HGVS:

NC_000018.10:g.51047044C>G
NG_013013.2:g.84005C>G
NM_005359.6:c.-3C>GMANE SELECT
LRG_318t1:c.-3C>G
LRG_318:g.84005C>G
NC_000018.9:g.48573414C>G
NM_005359.5:c.-3C>G

Links:

dbSNP: rs886053892

NCBI 1000 Genomes Browser:

rs886053892

Molecular consequence:

NM_005359.6:c.-3C>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]

Condition(s)

Name:: Hereditary cancer-predisposing syndrome
Synonyms:: Neoplastic Syndromes, Hereditary; Tumor predisposition; Cancer predisposition; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0015356; MeSH: D009386; MedGen: C0027672

Recent activity

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182654[uid] (1)
Taxonomy
PREDICTED: Sus scrofa SPARC like 1 (SPARCL1), transcript variant X5, mRNA
PREDICTED: Sus scrofa SPARC like 1 (SPARCL1), transcript variant X5, mRNA
gi|1191901203|ref|XM_021100261.1|

Nucleotide
Felimare villafranca voucher MNCN 15.05/70695 16S ribosomal RNA gene, partial se...
Felimare villafranca voucher MNCN 15.05/70695 16S ribosomal RNA gene, partial sequence; mitochondrial
gi|665990757|gb|KJ911272.1|

Nucleotide
Felimare villafranca voucher MNCN 15.05/70681 cytochrome c oxidase subunit I (CO...
Felimare villafranca voucher MNCN 15.05/70681 cytochrome c oxidase subunit I (COI) gene, partial cds; mitochondrial
gi|665990788|gb|KJ911288.1|

Nucleotide
NA [Influenza A virus (A/chicken/Taiwan/2838V/00(H6N1))]
NA [Influenza A virus (A/chicken/Taiwan/2838V/00(H6N1))]
gi|149794998|gb|ABR31786.1|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000913105	Color Diagnostics, LLC DBA Color Health	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Jan 18, 2023)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 25980754, 25741868

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000913105

Color Diagnostics, LLC DBA Color Health

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Jan 18, 2023)

germline

clinical testing

PubMed (2)
[See all records that cite these PMIDs]

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

Identification of a Variety of Mutations in Cancer Predisposition Genes in Patients With Suspected Lynch Syndrome.

Yurgelun MB, Allen B, Kaldate RR, Bowles KR, Judkins T, Kaushik P, Roa BB, Wenstrup RJ, Hartman AR, Syngal S.

Gastroenterology. 2015 Sep;149(3):604-13.e20. doi: 10.1053/j.gastro.2015.05.006. Epub 2015 May 14.

PubMed [citation]

PMID:: 25980754
PMCID:: PMC4550537

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

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.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Color Diagnostics, LLC DBA Color Health, SCV000913105.4

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

Description

This variant is located at the -3 position in the 5' untranslated region of the SMAD4 gene. To our knowledge, functional studies have not been performed for this variant. This variant has been reported in an individual affected with Lynch syndrome-associated cancer and/or polyps (PMID: 25980754). This variant has also been identified in 2/251154 chromosomes in the general population by the Genome Aggregation Database (gnomAD). The available evidence is insufficient to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance.

#	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

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