7-55156645-G-T

Variant names:

• chr7-55156645-G-T
• rs2302536
• NM_005228.5:c.1119G>T

Variant summary

Our verdict is Likely benign. The variant received -5 ACMG points: 2P and 7B. PM2 BP4_Strong BP6_Moderate BP7

The NM_005228.5(EGFR):​c.1119G>T​(p.Pro373Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. P373P) has been classified as Likely benign.

• Frequency: Genomes: not found (cov: 33)
• Consequence: EGFR NM_005228.5 synonymous
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -4.11
• Publications: 0 publications found

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 Gene-Disease associations (from GenCC):

• lung cancer

  Inheritance: AD Classification: DEFINITIVE Submitted by: G2P, Ambry Genetics
• non-small cell lung carcinoma

  Inheritance: AD Classification: DEFINITIVE Submitted by: ClinGen
• inflammatory skin and bowel disease, neonatal, 2

  Inheritance: AR Classification: STRONG, MODERATE, LIMITED Submitted by: Genomics England PanelApp, Labcorp Genetics (formerly Invitae), Ambry Genetics, G2P
• neonatal inflammatory skin and bowel disease

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Likely_benign. The variant received -5 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BP6: Variant 7-55156645-G-T is Benign according to our data. Variant chr7-55156645-G-T is described in CliVar as Likely_benign. Clinvar id is 4016738.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr7-55156645-G-T is described in CliVar as Likely_benign. Clinvar id is 4016738.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr7-55156645-G-T is described in CliVar as Likely_benign. Clinvar id is 4016738.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr7-55156645-G-T is described in CliVar as Likely_benign. Clinvar id is 4016738.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr7-55156645-G-T is described in CliVar as Likely_benign. Clinvar id is 4016738.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr7-55156645-G-T is described in CliVar as Likely_benign. Clinvar id is 4016738.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr7-55156645-G-T is described in CliVar as Likely_benign. Clinvar id is 4016738.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr7-55156645-G-T is described in CliVar as Likely_benign. Clinvar id is 4016738.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr7-55156645-G-T is described in CliVar as Likely_benign. Clinvar id is 4016738.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr7-55156645-G-T is described in CliVar as Likely_benign. Clinvar id is 4016738.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr7-55156645-G-T is described in CliVar as Likely_benign. Clinvar id is 4016738.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr7-55156645-G-T is described in CliVar as Likely_benign. Clinvar id is 4016738.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr7-55156645-G-T is described in CliVar as Likely_benign. Clinvar id is 4016738.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr7-55156645-G-T is described in CliVar as Likely_benign. Clinvar id is 4016738.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr7-55156645-G-T is described in CliVar as Likely_benign. Clinvar id is 4016738.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr7-55156645-G-T is described in CliVar as Likely_benign. Clinvar id is 4016738.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr7-55156645-G-T is described in CliVar as Likely_benign. Clinvar id is 4016738.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr7-55156645-G-T is described in CliVar as Likely_benign. Clinvar id is 4016738.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr7-55156645-G-T is described in CliVar as Likely_benign. Clinvar id is 4016738.Status of the report is criteria_provided_single_submitter, 1 stars.
• BP7: Synonymous conserved (PhyloP=-4.11 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EGFR	NM_005228.5	c.1119G>T	p.Pro373Pro	synonymous_variant	Exon 9 of 28	ENST00000275493.7	NP_005219.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EGFR	ENST00000275493.7	c.1119G>T	p.Pro373Pro	synonymous_variant	Exon 9 of 28	1	NM_005228.5	ENSP00000275493.2

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 33

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

Hereditary cancer-predisposing syndrome Benign:1

Apr 13, 2025

Ambry Genetics

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	0.041
DANN	Benign	0.77
PhyloP100		-4.1

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs2302536; hg19: chr7-55224338; COSMIC: COSV51797487;