7-55020559-TACACACACACACAC-TACACACACACACACACAC

Position:

• chr7-55020559-TACACACACACACAC-TACACACACACACACACAC

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.

The NM_005228.5(EGFR):​c.88+1225_88+1228dupACAC variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.15 (1679 hom., cov: 0)
  • Failed GnomAD Quality Control
• Consequence: EGFR NM_005228.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.306

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 (HGNC:):

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
EGFR	NM_005228.5	c.88+1225_88+1228dupACAC		intron_variant		ENST00000275493.7	NP_005219.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
EGFR	ENST00000275493.7	c.88+1225_88+1228dupACAC		intron_variant		1	NM_005228.5	ENSP00000275493.2

Frequencies

GnomAD3 genomes AF: 0.145 AC: 21041 AN: 144986 Hom.: 1676 Cov.: 0

Gnomad AFR AF: 0.0730

Gnomad AMI AF: 0.119

Gnomad AMR AF: 0.196

Gnomad ASJ AF: 0.109

Gnomad EAS AF: 0.0205

Gnomad SAS AF: 0.0718

Gnomad FIN AF: 0.216

Gnomad MID AF: 0.0752

Gnomad NFE AF: 0.184

Gnomad OTH AF: 0.124

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

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.145 AC: 21054 AN: 145076 Hom.: 1679 Cov.: 0 AF XY: 0.146 AC XY: 10301 AN XY: 70326

Gnomad4 AFR AF: 0.0730

Gnomad4 AMR AF: 0.196

Gnomad4 ASJ AF: 0.109

Gnomad4 EAS AF: 0.0206

Gnomad4 SAS AF: 0.0715

Gnomad4 FIN AF: 0.216

Gnomad4 NFE AF: 0.184

Gnomad4 OTH AF: 0.124

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11568315; hg19: chr7-55088252;