NM_004364.5(CEBPA):c.100C>A (p.Pro34Thr) AND Acute myeloid leukemia

Germline classification:: Uncertain significance (2 submissions)
Last evaluated:: Aug 30, 2023
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV001338310.7

Allele description [Variation Report for NM_004364.5(CEBPA):c.100C>A (p.Pro34Thr)]

NM_004364.5(CEBPA):c.100C>A (p.Pro34Thr)

Gene:

CEBPA:CCAAT enhancer binding protein alpha [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

19q13.11

Genomic location:

Preferred name:

NM_004364.5(CEBPA):c.100C>A (p.Pro34Thr)

HGVS:

NC_000019.10:g.33302315G>T
NG_012022.1:g.5210C>A
NM_001285829.2:c.-258C>A
NM_001287424.2:c.205C>A
NM_001287435.2:c.58C>A
NM_004364.3:c.100C>A
NM_004364.5:c.100C>AMANE SELECT
NP_001274353.1:p.Pro69Thr
NP_001274364.1:p.Pro20Thr
NP_004355.2:p.Pro34Thr
LRG_456t1:c.100C>A
LRG_456:g.5210C>A
NC_000019.9:g.33793221G>T
NM_004364.5:c.100C>A

Protein change:

P20T

Links:

dbSNP: rs996435066

NCBI 1000 Genomes Browser:

rs996435066

Molecular consequence:

NM_001285829.2:c.-258C>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001287424.2:c.205C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001287435.2:c.58C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_004364.5:c.100C>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Acute myeloid leukemia (AML)
Synonyms:: Acute myeloid leukemia, adult; AML adult; Acute myelogenous leukemia; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0018874; MeSH: D015470; MedGen: C0023467; Orphanet: 519; OMIM: 601626; Human Phenotype Ontology: HP:0004808

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001531971	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Apr 19, 2023)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV004212557	Baylor Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Aug 30, 2023)	unknown	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

SCV001531971

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Apr 19, 2023)

germline

clinical testing

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

SCV004212557

Baylor Genetics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Aug 30, 2023)

unknown

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
not provided	unknown	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

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 Labcorp Genetics (formerly Invitae), Labcorp, SCV001531971.4

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

Description

In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant¬† is likely to be tolerated. ClinVar contains an entry for this variant (Variation ID: 1035441). This variant has not been reported in the literature in individuals affected with CEBPA-related conditions. This variant is present in population databases (no rsID available, gnomAD 0.008%). This sequence change replaces proline, which is neutral and non-polar, with threonine, which is neutral and polar, at codon 34 of the CEBPA protein (p.Pro34Thr).

#	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 Baylor Genetics, SCV004212557.1

#	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	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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