rs6593205

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_005228.5(EGFR):​c.89-41287A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.681 in 152,206 control chromosomes in the GnomAD database, including 35,919 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.68 ( 35919 hom., cov: 34)

Consequence

EGFR
NM_005228.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.07
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.97).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.875 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
EGFRNM_005228.5 linkuse as main transcriptc.89-41287A>G intron_variant ENST00000275493.7

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
EGFRENST00000275493.7 linkuse as main transcriptc.89-41287A>G intron_variant 1 NM_005228.5 P1P00533-1

Frequencies

GnomAD3 genomes
AF:
0.681
AC:
103549
AN:
152088
Hom.:
35901
Cov.:
34
show subpopulations
Gnomad AFR
AF:
0.799
Gnomad AMI
AF:
0.675
Gnomad AMR
AF:
0.657
Gnomad ASJ
AF:
0.672
Gnomad EAS
AF:
0.897
Gnomad SAS
AF:
0.704
Gnomad FIN
AF:
0.605
Gnomad MID
AF:
0.722
Gnomad NFE
AF:
0.609
Gnomad OTH
AF:
0.668
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.681
AC:
103614
AN:
152206
Hom.:
35919
Cov.:
34
AF XY:
0.684
AC XY:
50892
AN XY:
74410
show subpopulations
Gnomad4 AFR
AF:
0.799
Gnomad4 AMR
AF:
0.657
Gnomad4 ASJ
AF:
0.672
Gnomad4 EAS
AF:
0.897
Gnomad4 SAS
AF:
0.703
Gnomad4 FIN
AF:
0.605
Gnomad4 NFE
AF:
0.609
Gnomad4 OTH
AF:
0.663
Alfa
AF:
0.650
Hom.:
8240
Bravo
AF:
0.687
Asia WGS
AF:
0.774
AC:
2691
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.97
CADD
Benign
0.23
DANN
Benign
0.25

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs6593205; hg19: chr7-55168692; API