rs1057519861

Variant names:

• chr7-55181398-T-A
• rs1057519861
• NM_005228.5:c.2389T>A

Your query was ambiguous. Multiple possible variants found:

• chr7-55181398-T-A
• chr7-55181398-T-C
• chr7-55181398-T-G

Variant summary

Our verdict is Uncertain significance. The variant received 3 ACMG points: 3P and 0B. PM2 PP3

The ENST00000275493.7(EGFR):​c.2389T>A​(p.Cys797Ser) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another nucleotide change resulting in the same amino acid substitution has been previously reported as Uncertain significance in ClinVar. Synonymous variant affecting the same amino acid position (i.e. C797C) has been classified as Likely benign.

• Frequency: Genomes: not found (cov: 33)
• Consequence: EGFR ENST00000275493.7 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 6.25
• Publications: 1646 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-AS1 (HGNC:40207): (EGFR antisense RNA 1)

ACMG classification

Our verdict: Uncertain_significance. The variant received 3 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.787

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000275493.7. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EGFR	NM_005228.5	MANE Select	c.2389T>A	p.Cys797Ser	missense	Exon 20 of 28	NP_005219.2
	EGFR	NM_001346899.2		c.2254T>A	p.Cys752Ser	missense	Exon 19 of 27	NP_001333828.1
	EGFR	NM_001346900.2		c.2230T>A	p.Cys744Ser	missense	Exon 20 of 28	NP_001333829.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EGFR	ENST00000275493.7	TSL:1 MANE Select	c.2389T>A	p.Cys797Ser	missense	Exon 20 of 28	ENSP00000275493.2
	EGFR	ENST00000455089.5	TSL:1	c.2254T>A	p.Cys752Ser	missense	Exon 19 of 26	ENSP00000415559.1
	EGFR	ENST00000450046.2	TSL:4	c.2230T>A	p.Cys744Ser	missense	Exon 20 of 28	ENSP00000413354.2

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 33

GnomAD4 genome Cov.: 33

ClinVar

ClinVar submissions as Germline

Significance: Uncertain significance

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	1	-	EGFR-related lung cancer (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.74
BayesDel_addAF	Pathogenic	0.24	D
BayesDel_noAF	Uncertain	0.11
CADD	Pathogenic	26
DANN	Benign	0.96
DEOGEN2	Uncertain	0.71	D
Eigen	Benign	0.057
Eigen_PC	Uncertain	0.28
FATHMM_MKL	Uncertain	0.96	D
LIST_S2	Uncertain	0.92	D
M_CAP	Benign	0.029	D
MetaRNN	Pathogenic	0.79	D
MetaSVM	Benign	-0.70	T
MutationAssessor	Benign	-1.4	N
PhyloP100		6.3
PrimateAI	Uncertain	0.71	T
PROVEAN	Pathogenic	-7.9	D
REVEL	Uncertain	0.45
Sift	Benign	0.40	T
Sift4G	Benign	0.27	T
Polyphen		0.45	B
Vest4		0.86
MutPred		0.57		Loss of catalytic residue at L798 (P = 0.0191)
MVP		0.89
MPC		1.6
ClinPred		0.94	D
GERP RS		5.9
Varity_R		0.92
gMVP		0.75
Mutation Taster		=7/93	disease causing

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

Other links and lift over

dbSNP: rs1057519861; hg19: chr7-55249091;