7-55191792-C-T

Position:

chr7-55191792-C-T

Variant summary

Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP6BS1

The NM_005228.5(EGFR):c.2543C>T(p.Pro848Leu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000373 in 1,613,922 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

Frequency

Genomes: 𝑓 0.00026 ( 0 hom., cov: 32)

Exomes 𝑓: 0.00039 ( 0 hom. )

Consequence

EGFR
NM_005228.5 missense

Scores

Clinical Significance

Conflicting classifications of pathogenicity criteria provided, conflicting classifications U:4B:4O:1

Conservation

PhyloP100: 7.85

Variant links:

Genes affected

EGFR (HGNC:3236): (epidermal growth factor receptor) The protein encoded by this gene is a transmembrane glycoprotein that is a member of the protein kinase superfamily. This protein is a receptor for members of the epidermal growth factor family. EGFR is a cell surface protein that binds to epidermal growth factor, thus inducing receptor dimerization and tyrosine autophosphorylation leading to cell proliferation. Mutations in this gene are associated with lung cancer. EGFR is a component of the cytokine storm which contributes to a severe form of Coronavirus Disease 2019 (COVID-19) resulting from infection with severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). [provided by RefSeq, Jul 2020]

EGFR links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -3 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP6

Variant 7-55191792-C-T is Benign according to our data. Variant chr7-55191792-C-T is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 45282.We mark this variant Likely_benign, oryginal submissions are: {Likely_benign=3, not_provided=1, Benign=1, Uncertain_significance=3}.

BS1

Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.000256 (39/152068) while in subpopulation NFE AF= 0.000485 (33/68034). AF 95% confidence interval is 0.000354. There are 0 homozygotes in gnomad4. There are 17 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
EGFR	NM_005228.5 linkuse as main transcript	c.2543C>T	p.Pro848Leu	missense_variant	21/28	ENST00000275493.7	NP_005219.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
EGFR	ENST00000275493.7 linkuse as main transcript	c.2543C>T	p.Pro848Leu	missense_variant	21/28	1	NM_005228.5	ENSP00000275493	P1	P00533-1
EGFR	ENST00000455089.5 linkuse as main transcript	c.2408C>T	p.Pro803Leu	missense_variant	20/26	1		ENSP00000415559
EGFR	ENST00000450046.2 linkuse as main transcript	c.2384C>T	p.Pro795Leu	missense_variant	21/28	4		ENSP00000413354
EGFR	ENST00000700145.1 linkuse as main transcript	c.893C>T	p.Pro298Leu	missense_variant	8/9			ENSP00000514824

Frequencies

GnomAD3 genomes

AF:

0.000256

AC:

AN:

152068

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0000483

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000197

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.000194

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000485

Gnomad OTH

AF:

0.00

GnomAD3 exomes

AF:

0.000358

AC:

AN:

251310

Hom.:

AF XY:

0.000383

AC XY:

AN XY:

135816

show subpopulations

Gnomad AFR exome

AF:

0.0000616

Gnomad AMR exome

AF:

0.000173

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.0000544

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.000232

Gnomad NFE exome

AF:

0.000642

Gnomad OTH exome

AF:

0.000652

GnomAD4 exome

AF:

0.000385

AC:

563

AN:

1461854

Hom.:

Cov.:

AF XY:

0.000402

AC XY:

292

AN XY:

727228

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.000134

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.0000504

Gnomad4 SAS exome

AF:

0.0000116

Gnomad4 FIN exome

AF:

0.000300

Gnomad4 NFE exome

AF:

0.000466

Gnomad4 OTH exome

AF:

0.000331

GnomAD4 genome

AF:

0.000256

AC:

AN:

152068

Hom.:

Cov.:

AF XY:

0.000229

AC XY:

AN XY:

74266

show subpopulations

Gnomad4 AFR

AF:

0.0000483

Gnomad4 AMR

AF:

0.000197

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.000194

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000485

Gnomad4 OTH

AF:

0.00

Alfa

AF:

0.000437

Hom.:

Bravo

AF:

0.000272

TwinsUK

AF:

0.000809

AC:

ALSPAC

AF:

0.000259

AC:

ESP6500AA

AF:

0.00

AC:

ESP6500EA

AF:

0.000698

AC:

ExAC

AF:

0.000461

AC:

EpiCase

AF:

0.000654

EpiControl

AF:

0.000356

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Uncertain:4Benign:4Other:1

Revision: criteria provided, conflicting classifications

LINK: link

Submissions by phenotype

not provided

Uncertain:2Benign:1

Uncertain significance, criteria provided, single submitter	clinical testing	Institute for Clinical Genetics, University Hospital TU Dresden, University Hospital TU Dresden	Nov 03, 2021	- -
Uncertain significance, criteria provided, single submitter	clinical testing	GeneDx	Mar 14, 2022	In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Identified in the germline of individuals with lung cancer, glioma, and retinoblastoma (Sequist 2006, Prim 2014, Akhavanfard 2021); Published functional studies demonstrate reduced/absent auto-phosphorylation, kinase activity, and capacity to bind c-Cbl (de Gunst 2007, Sarcar 2019); This variant is associated with the following publications: (PMID: 22848293, 17877814, 25176975, 16857818, 33326033, 31314158) -
Benign, criteria provided, single submitter	clinical testing	Quest Diagnostics Nichols Institute San Juan Capistrano	May 01, 2023	- -

not specified

Uncertain:1Benign:1

Likely benign, criteria provided, single submitter	clinical testing	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	Jul 11, 2013	Pro848Leu variant in Exon 21 of EGFR: This variant is not expected to have clinical significance because iIn vitro studies suggest that this variant does not activate EGFR activity and does not render the protein sensitive to tyrosine kinase inhibitors (TKIs) (De Gunst 2007, Han 2011). It has been previously identified in both tumor and normal tissue in an individuals with lung cancer (Sequist 2007), and it has been identified in 0.06% (6/8600) of European American chromosomes by the NHLBI Exome Sequencing Project (http://evs.gs.washington.edu/EVS/; dbSNP rs148934350). -
Uncertain significance, no assertion criteria provided	clinical testing	Genetic Services Laboratory, University of Chicago	Jun 08, 2022	DNA sequence analysis of the EGFR gene demonstrated a sequence change, c.2543C>T, in exon 21 that results in an amino acid change, p.Pro848Leu. This sequence change has been previously described in individuals with non-small cell lung cancer (NSCLC) (PMID: 25176975,16857818,22848293). In vitro functional studies have suggested that this variant is not a kinase activating mutation and showed a response to tyrosine kinase inhibitors, similar to the wild-type (PMID: 17877814, 22848293). This sequence change has been described in the gnomAD database with a frequency of 0.06% in the European subpopulation (dbSNP rs148934350). The p.Pro848Leu change affects a highly conserved amino acid residue located in a domain of the EGFR protein that is known to be functional. In-silico pathogenicity prediction tools (SIFT, PolyPhen2, Align GVGD, REVEL) provide contradictory results for the p.Pro848Leu substitution. Due to insufficient evidences and the lack of functional studies, the clinical significance of the p.Pro848Leu change remains unknown at this time. -

Hereditary cancer-predisposing syndrome

Uncertain:1

Uncertain significance, criteria provided, single submitter

curation

Sema4, Sema4

Nov 01, 2021

- -

Lung carcinoma

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Mendelics

May 28, 2019

- -

EGFR-related lung cancer

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jan 18, 2024

- -

Lung cancer

Other:1

not provided, no classification provided

phenotyping only

GenomeConnect - Invitae Patient Insights Network

Variant interpreted as Uncertain significance and reported on 11-11-2019 by Lab Invitae. GenomeConnect-Invitae Patient Insights Network assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. Registry team members make no attempt to reinterpret the clinical significance of the variant. Phenotypic details are available under supporting information. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Pathogenic

0.74

BayesDel_addAF

Benign

-0.067

BayesDel_noAF

Uncertain

0.030

CADD

Pathogenic

DANN

Uncertain

1.0

DEOGEN2

Uncertain

0.71

D;D;D

Eigen

Uncertain

0.50

Eigen_PC

Uncertain

0.47

FATHMM_MKL

Pathogenic

0.98

LIST_S2

Uncertain

0.95

D;D;D

M_CAP

Uncertain

0.14

MetaRNN

Uncertain

0.54

D;D;D

MetaSVM

Benign

-0.39

MutationAssessor

Benign

0.37

.;.;N

MutationTaster

Benign

1.0

D;D;D;D

PrimateAI

Pathogenic

0.89

PROVEAN

Pathogenic

-8.9

D;.;D

REVEL

Uncertain

0.47

Sift

Uncertain

0.0010

D;.;D

Sift4G

Uncertain

0.046

D;T;D

Polyphen

1.0

D;.;D

Vest4

0.73

MVP

0.84

MPC

1.5

ClinPred

0.22

GERP RS

5.8

Varity_R

0.95

gMVP

0.82

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over