Variant 7-55146750-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_005228.5(EGFR):c.559+10G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0865 in 1,613,864 control chromosomes in the GnomAD database, including 6,618 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.065 ( 418 hom., cov: 33)

Exomes 𝑓: 0.089 ( 6200 hom. )

Consequence

EGFR
NM_005228.5 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:5

Conservation

PhyloP100: -2.81

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]

EGFR links:

EGFR (HGNC:):

EGFR links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.83).

BP6

Variant 7-55146750-G-A is Benign according to our data. Variant chr7-55146750-G-A is described in ClinVar as [Benign]. Clinvar id is 259681.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0929 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
EGFR	NM_005228.5 linkuse as main transcript	c.559+10G>A		intron_variant		ENST00000275493.7	NP_005219.2	P00533-1Q504U8F2YGG7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
EGFR	ENST00000275493.7 linkuse as main transcript	c.559+10G>A		intron_variant		1	NM_005228.5	ENSP00000275493.2		P00533-1

Frequencies

GnomAD3 genomes

AF:

0.0646

AC:

9829

AN:

152118

Hom.:

414

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0206

Gnomad AMI

AF:

0.0570

Gnomad AMR

AF:

0.0594

Gnomad ASJ

AF:

0.0974

Gnomad EAS

AF:

0.0553

Gnomad SAS

AF:

0.100

Gnomad FIN

AF:

0.0510

Gnomad MID

AF:

0.0380

Gnomad NFE

AF:

0.0911

Gnomad OTH

AF:

0.0769

GnomAD3 exomes

AF:

0.0762

AC:

19130

AN:

251086

Hom.:

819

AF XY:

0.0805

AC XY:

10932

AN XY:

135728

show subpopulations

Gnomad AFR exome

AF:

0.0179

Gnomad AMR exome

AF:

0.0412

Gnomad ASJ exome

AF:

0.0950

Gnomad EAS exome

AF:

0.0668

Gnomad SAS exome

AF:

0.106

Gnomad FIN exome

AF:

0.0492

Gnomad NFE exome

AF:

0.0917

Gnomad OTH exome

AF:

0.0837

GnomAD4 exome

AF:

0.0888

AC:

129804

AN:

1461628

Hom.:

6200

Cov.:

AF XY:

0.0896

AC XY:

65123

AN XY:

727116

show subpopulations

Gnomad4 AFR exome

AF:

0.0163

Gnomad4 AMR exome

AF:

0.0436

Gnomad4 ASJ exome

AF:

0.0976

Gnomad4 EAS exome

AF:

0.0494

Gnomad4 SAS exome

AF:

0.106

Gnomad4 FIN exome

AF:

0.0528

Gnomad4 NFE exome

AF:

0.0948

Gnomad4 OTH exome

AF:

0.0829

GnomAD4 genome

AF:

0.0647

AC:

9843

AN:

152236

Hom.:

418

Cov.:

AF XY:

0.0636

AC XY:

4737

AN XY:

74440

show subpopulations

Gnomad4 AFR

AF:

0.0205

Gnomad4 AMR

AF:

0.0593

Gnomad4 ASJ

AF:

0.0974

Gnomad4 EAS

AF:

0.0552

Gnomad4 SAS

AF:

0.100

Gnomad4 FIN

AF:

0.0510

Gnomad4 NFE

AF:

0.0911

Gnomad4 OTH

AF:

0.0832

Alfa

AF:

0.0841

Hom.:

521

Bravo

AF:

0.0632

Asia WGS

AF:

0.0960

AC:

334

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:5

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Feb 07, 2019	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

- -

EGFR-related lung cancer

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Feb 01, 2024

- -

Lung cancer

Benign:1

Benign, criteria provided, single submitter

clinical testing

KCCC/NGS Laboratory, Kuwait Cancer Control Center

Jul 07, 2023

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

0.12

DANN

Benign

0.41

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over