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NM_004064.5(CDKN1B):c.3G>A (p.Met1Ile) AND Hereditary cancer-predisposing syndrome

Germline classification:
Likely benign (1 submission)
Last evaluated:
Aug 1, 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:
RCV002377114.2

Allele description [Variation Report for NM_004064.5(CDKN1B):c.3G>A (p.Met1Ile)]

NM_004064.5(CDKN1B):c.3G>A (p.Met1Ile)

Gene:
CDKN1B:cyclin dependent kinase inhibitor 1B [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
12p13.1
Genomic location:
Preferred name:
NM_004064.5(CDKN1B):c.3G>A (p.Met1Ile)
HGVS:
  • NC_000012.12:g.12717842G>A
  • NG_016341.1:g.5475G>A
  • NM_004064.5:c.3G>AMANE SELECT
  • NP_004055.1:p.Met1Ile
  • NP_004055.1:p.Met1Ile
  • NC_000012.11:g.12870776G>A
  • NM_004064.3:c.3G>A
  • NM_004064.4:c.3G>A
Protein change:
M1I
Links:
dbSNP: rs756190836
NCBI 1000 Genomes Browser:
rs756190836
Molecular consequence:
  • NM_004064.5:c.3G>A - initiator_codon_variant - [Sequence Ontology: SO:0001582]
  • NM_004064.5:c.3G>A - missense variant - [Sequence Ontology: SO:0001583]

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

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002625324Ambry Genetics
criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)		Likely benign
(Aug 1, 2022) 		germlineclinical testing

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

Citation Link

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Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Pathogenic Germline Variants in 10,389 Adult Cancers.

Huang KL, Mashl RJ, Wu Y, Ritter DI, Wang J, Oh C, Paczkowska M, Reynolds S, Wyczalkowski MA, Oak N, Scott AD, Krassowski M, Cherniack AD, Houlahan KE, Jayasinghe R, Wang LB, Zhou DC, Liu D, Cao S, Kim YW, Koire A, McMichael JF, et al.

Cell. 2018 Apr 5;173(2):355-370.e14. doi: 10.1016/j.cell.2018.03.039.

PubMed [citation]
PMID:
29625052
PMCID:
PMC5949147

Details of each submission

From Ambry Genetics, SCV002625324.3

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

Description

This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Oct 13, 2024