7-55020559-TACACACACACACAC-TACACACACACACACACACACAC

Position:

• chr7-55020559-TACACACACACACAC-TACACACACACACACACACACAC

Variant summary

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

The NM_005228.5(EGFR):​c.88+1221_88+1228dup 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 0.22 (3686 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]

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+1221_88+1228dup		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+1221_88+1228dup		intron_variant		1	NM_005228.5	ENSP00000275493	P1

Frequencies

GnomAD3 genomes AF: 0.00 AC: 31301 AN: 144896 Hom.: 3687 Cov.: 0 FAILED QC

Gnomad AFR AF: 0.140

Gnomad AMI AF: 0.273

Gnomad AMR AF: 0.246

Gnomad ASJ AF: 0.210

Gnomad EAS AF: 0.535

Gnomad SAS AF: 0.256

Gnomad FIN AF: 0.304

Gnomad MID AF: 0.135

Gnomad NFE AF: 0.216

Gnomad OTH AF: 0.200

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: 0.216 AC: 31301 AN: 144984 Hom.: 3686 Cov.: 0 AF XY: 0.221 AC XY: 15560 AN XY: 70270

Gnomad4 AFR AF: 0.140

Gnomad4 AMR AF: 0.247

Gnomad4 ASJ AF: 0.210

Gnomad4 EAS AF: 0.534

Gnomad4 SAS AF: 0.257

Gnomad4 FIN AF: 0.304

Gnomad4 NFE AF: 0.216

Gnomad4 OTH AF: 0.198

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;