rs2110290

Variant summary

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

The NM_005228.5(EGFR):​c.89-37211T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.325 in 152,114 control chromosomes in the GnomAD database, including 8,852 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 0.32 ( 8852 hom., cov: 33)

Consequence

EGFR
NM_005228.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.15
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=-0.84).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.687 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
EGFRNM_005228.5 linkuse as main transcriptc.89-37211T>C intron_variant ENST00000275493.7

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
EGFRENST00000275493.7 linkuse as main transcriptc.89-37211T>C intron_variant 1 NM_005228.5 P1P00533-1

Frequencies

GnomAD3 genomes
AF:
0.325
AC:
49402
AN:
151996
Hom.:
8863
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.243
Gnomad AMI
AF:
0.420
Gnomad AMR
AF:
0.374
Gnomad ASJ
AF:
0.284
Gnomad EAS
AF:
0.706
Gnomad SAS
AF:
0.392
Gnomad FIN
AF:
0.404
Gnomad MID
AF:
0.342
Gnomad NFE
AF:
0.320
Gnomad OTH
AF:
0.300
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.325
AC:
49396
AN:
152114
Hom.:
8852
Cov.:
33
AF XY:
0.335
AC XY:
24879
AN XY:
74354
show subpopulations
Gnomad4 AFR
AF:
0.242
Gnomad4 AMR
AF:
0.374
Gnomad4 ASJ
AF:
0.284
Gnomad4 EAS
AF:
0.706
Gnomad4 SAS
AF:
0.391
Gnomad4 FIN
AF:
0.404
Gnomad4 NFE
AF:
0.320
Gnomad4 OTH
AF:
0.297
Alfa
AF:
0.324
Hom.:
16730
Bravo
AF:
0.318
Asia WGS
AF:
0.499
AC:
1734
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.84
CADD
Benign
12
DANN
Benign
0.73

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: rs2110290; hg19: chr7-55172768; API