NM_005228.5(EGFR):c.2972G>C (p.Ser991Thr) AND EGFR-related lung cancer

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Dec 12, 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:: RCV002046135.6

Allele description [Variation Report for NM_005228.5(EGFR):c.2972G>C (p.Ser991Thr)]

NM_005228.5(EGFR):c.2972G>C (p.Ser991Thr)

Gene:

EGFR:epidermal growth factor receptor [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

7p11.2

Genomic location:

Preferred name:

NM_005228.5(EGFR):c.2972G>C (p.Ser991Thr)

HGVS:

NC_000007.14:g.55201213G>C
NG_007726.3:g.187182G>C
NM_001346897.2:c.2837G>C
NM_001346898.2:c.2972G>C
NM_001346899.2:c.2837G>C
NM_001346900.2:c.2813G>C
NM_001346941.2:c.2171G>C
NM_005228.5:c.2972G>CMANE SELECT
NP_001333826.1:p.Ser946Thr
NP_001333827.1:p.Ser991Thr
NP_001333828.1:p.Ser946Thr
NP_001333829.1:p.Ser938Thr
NP_001333870.1:p.Ser724Thr
NP_005219.2:p.Ser991Thr
LRG_304:g.187182G>C
NC_000007.13:g.55268906G>C

Protein change:

S724T

Links:

dbSNP: rs1787831699

NCBI 1000 Genomes Browser:

rs1787831699

Molecular consequence:

NM_001346897.2:c.2837G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001346898.2:c.2972G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001346899.2:c.2837G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001346900.2:c.2813G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001346941.2:c.2171G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_005228.5:c.2972G>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: EGFR-related lung cancer (EGFR)
Identifiers:: MedGen: CN130014

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MAG: Candidatus Colwellbacteria bacterium CG10_big_fil_rev_8_21_14_0_10_42_22, w...
MAG: Candidatus Colwellbacteria bacterium CG10_big_fil_rev_8_21_14_0_10_42_22, whole genome shotgun sequencing project
gi|1277202558|gb|PFAH00000000.1|PFA 0000

Nucleotide
zinc finger protein AEBP2 isoform X2 [Homo sapiens]
zinc finger protein AEBP2 isoform X2 [Homo sapiens]
gi|2217287458|ref|XP_047284254.1|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002312024	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Dec 12, 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

SCV002312024

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Dec 12, 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, SCV002312024.3

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

Description

This variant is not present in population databases (gnomAD no frequency). 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. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt EGFR protein function. ClinVar contains an entry for this variant (Variation ID: 1520696). This variant has not been reported in the literature in individuals affected with EGFR-related conditions. This sequence change replaces serine, which is neutral and polar, with threonine, which is neutral and polar, at codon 991 of the EGFR protein (p.Ser991Thr).

#	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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