rs2241054

Variant summary

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

The NM_005228.5(EGFR):​c.1920-697G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.241 in 152,108 control chromosomes in the GnomAD database, including 5,297 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 0.24 ( 5297 hom., cov: 33)

Consequence

EGFR
NM_005228.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.408
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=-0.93).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.536 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
EGFRNM_005228.5 linkuse as main transcriptc.1920-697G>A intron_variant ENST00000275493.7

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
EGFRENST00000275493.7 linkuse as main transcriptc.1920-697G>A intron_variant 1 NM_005228.5 P1P00533-1
EGFRENST00000455089.5 linkuse as main transcriptc.1785-697G>A intron_variant 1
EGFRENST00000450046.2 linkuse as main transcriptc.1761-697G>A intron_variant 4
EGFRENST00000700145.1 linkuse as main transcriptc.269-697G>A intron_variant

Frequencies

GnomAD3 genomes
AF:
0.241
AC:
36588
AN:
151990
Hom.:
5295
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0924
Gnomad AMI
AF:
0.262
Gnomad AMR
AF:
0.274
Gnomad ASJ
AF:
0.348
Gnomad EAS
AF:
0.553
Gnomad SAS
AF:
0.376
Gnomad FIN
AF:
0.311
Gnomad MID
AF:
0.294
Gnomad NFE
AF:
0.273
Gnomad OTH
AF:
0.252
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.241
AC:
36595
AN:
152108
Hom.:
5297
Cov.:
33
AF XY:
0.248
AC XY:
18420
AN XY:
74338
show subpopulations
Gnomad4 AFR
AF:
0.0923
Gnomad4 AMR
AF:
0.274
Gnomad4 ASJ
AF:
0.348
Gnomad4 EAS
AF:
0.553
Gnomad4 SAS
AF:
0.376
Gnomad4 FIN
AF:
0.311
Gnomad4 NFE
AF:
0.273
Gnomad4 OTH
AF:
0.253
Alfa
AF:
0.271
Hom.:
2813
Bravo
AF:
0.234
Asia WGS
AF:
0.422
AC:
1466
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.93
CADD
Benign
0.064
DANN
Benign
0.53

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: rs2241054; hg19: chr7-55239979; API