rs397509368

Variant names:

• chr7-55174776-TTAAGAGAAGCAA-C
• rs397509368
• NM_005228.5:c.2239_2251delTTAAGAGAAGCAAinsC

Variant summary

Our verdict is Uncertain significance. The variant received 5 ACMG points: 5P and 0B. PM1 PM4 PP3

The NM_005228.5(EGFR):​c.2239_2251delTTAAGAGAAGCAAinsC​(p.Leu747_Thr751delinsPro) variant causes a disruptive inframe deletion, synonymous change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. Variant has been reported in ClinVar as drug response (no stars). Synonymous variant affecting the same amino acid position has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 33)
• Consequence: EGFR NM_005228.5 disruptive_inframe_deletion, synonymous
• Clinical Significance: drug response no assertion criteria provided O:2
• Conservation: PhyloP100: 9.89
• Publications: 3 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: Uncertain_significance. The variant received 5 ACMG points.

• PM1: In a hotspot region, there are 2 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 2 benign, 35 uncertain in NM_005228.5
• PM4: Nonframeshift variant in NON repetitive region in NM_005228.5.
• PP3: No computational evidence supports a deleterious effect, but strongly conserved according to phyloP

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EGFR	NM_005228.5	c.2239_2251delTTAAGAGAAGCAAinsC	p.Leu747_Thr751delinsPro	disruptive_inframe_deletion, synonymous_variant	Exon 19 of 28	ENST00000275493.7	NP_005219.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EGFR	ENST00000275493.7	c.2239_2251delTTAAGAGAAGCAAinsC	p.Leu747_Thr751delinsPro	disruptive_inframe_deletion, synonymous_variant	Exon 19 of 28	1	NM_005228.5	ENSP00000275493.2
EGFR	ENST00000455089.5	c.2104_2116delTTAAGAGAAGCAAinsC	p.Leu702_Thr706delinsPro	disruptive_inframe_deletion, synonymous_variant	Exon 18 of 26	1		ENSP00000415559.1
EGFR	ENST00000450046.2	c.2080_2092delTTAAGAGAAGCAAinsC	p.Leu694_Thr698delinsPro	disruptive_inframe_deletion, synonymous_variant	Exon 19 of 28	4		ENSP00000413354.2
EGFR	ENST00000700145.1	c.586_598delTTAAGAGAAGCAAinsC	p.Leu196_Thr200delinsPro	disruptive_inframe_deletion, synonymous_variant	Exon 6 of 9			ENSP00000514824.1

Frequencies

GnomAD3 genomes Cov.: 33

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 33

ClinVar

Significance: drug response

Submissions summary: Other:2

Revision: no assertion criteria provided

Submissions by phenotype

Nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, somatic Other:1

May 20, 2004

OMIM

Significance: drug response

Review Status: no assertion criteria provided

Collection Method: literature only

- -

Tyrosine kinase inhibitor response Other:1

Oct 28, 2006

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: drug response

Review Status: no assertion criteria provided

Collection Method: clinical testing

- Responsive

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		9.9

Splicing

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

Other links and lift over

dbSNP: rs397509368; hg19: chr7-55242469; COSMIC: COSV51765856;