chr7-55174143-C-T
Variant names:
Variant summary
Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_005228.5(EGFR):c.2184+100C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0422 in 1,513,934 control chromosomes in the GnomAD database, including 1,527 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.051 ( 225 hom., cov: 33)
Exomes 𝑓: 0.041 ( 1302 hom. )
Consequence
EGFR
NM_005228.5 intron
NM_005228.5 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.765
Publications
6 publications found
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 Gene-Disease associations (from GenCC):
- lung cancerInheritance: AD Classification: DEFINITIVE Submitted by: G2P, Ambry Genetics
- non-small cell lung carcinomaInheritance: AD Classification: DEFINITIVE Submitted by: ClinGen
- inflammatory skin and bowel disease, neonatal, 2Inheritance: AR Classification: STRONG, MODERATE, LIMITED Submitted by: Genomics England PanelApp, Labcorp Genetics (formerly Invitae), Ambry Genetics, G2P
- neonatal inflammatory skin and bowel diseaseInheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -20 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.86).
BP6
Variant 7-55174143-C-T is Benign according to our data. Variant chr7-55174143-C-T is described in ClinVar as [Benign]. Clinvar id is 1228216.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0759 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
EGFR | ENST00000275493.7 | c.2184+100C>T | intron_variant | Intron 18 of 27 | 1 | NM_005228.5 | ENSP00000275493.2 | |||
EGFR | ENST00000455089.5 | c.2049+100C>T | intron_variant | Intron 17 of 25 | 1 | ENSP00000415559.1 | ||||
EGFR | ENST00000450046.2 | c.2025+100C>T | intron_variant | Intron 18 of 27 | 4 | ENSP00000413354.2 | ||||
EGFR | ENST00000700145.1 | c.531+100C>T | intron_variant | Intron 5 of 8 | ENSP00000514824.1 |
Frequencies
GnomAD3 genomes AF: 0.0509 AC: 7743AN: 152210Hom.: 227 Cov.: 33 show subpopulations
GnomAD3 genomes
AF:
AC:
7743
AN:
152210
Hom.:
Cov.:
33
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.0413 AC: 56217AN: 1361606Hom.: 1302 AF XY: 0.0409 AC XY: 27607AN XY: 675406 show subpopulations
GnomAD4 exome
AF:
AC:
56217
AN:
1361606
Hom.:
AF XY:
AC XY:
27607
AN XY:
675406
show subpopulations
African (AFR)
AF:
AC:
2468
AN:
30560
American (AMR)
AF:
AC:
1149
AN:
35118
Ashkenazi Jewish (ASJ)
AF:
AC:
1619
AN:
23868
East Asian (EAS)
AF:
AC:
3
AN:
38190
South Asian (SAS)
AF:
AC:
1827
AN:
78304
European-Finnish (FIN)
AF:
AC:
916
AN:
47790
Middle Eastern (MID)
AF:
AC:
308
AN:
4470
European-Non Finnish (NFE)
AF:
AC:
45257
AN:
1046872
Other (OTH)
AF:
AC:
2670
AN:
56434
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.506
Heterozygous variant carriers
0
2605
5209
7814
10418
13023
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Exome Hom
Variant carriers
0
1666
3332
4998
6664
8330
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome AF: 0.0508 AC: 7745AN: 152328Hom.: 225 Cov.: 33 AF XY: 0.0491 AC XY: 3656AN XY: 74494 show subpopulations
GnomAD4 genome
AF:
AC:
7745
AN:
152328
Hom.:
Cov.:
33
AF XY:
AC XY:
3656
AN XY:
74494
show subpopulations
African (AFR)
AF:
AC:
3250
AN:
41568
American (AMR)
AF:
AC:
651
AN:
15310
Ashkenazi Jewish (ASJ)
AF:
AC:
266
AN:
3472
East Asian (EAS)
AF:
AC:
2
AN:
5186
South Asian (SAS)
AF:
AC:
106
AN:
4828
European-Finnish (FIN)
AF:
AC:
178
AN:
10620
Middle Eastern (MID)
AF:
AC:
33
AN:
294
European-Non Finnish (NFE)
AF:
AC:
3136
AN:
68026
Other (OTH)
AF:
AC:
120
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.497
Heterozygous variant carriers
0
385
771
1156
1542
1927
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
86
172
258
344
430
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
64
AN:
3478
ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
-
Breakthrough Genomics, Breakthrough Genomics
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:not provided
- -
Mar 16, 2019
GeneDx
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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