Variant 7-55151466-C-T 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.628+104C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.528 in 1,206,082 control chromosomes in the GnomAD database, including 170,404 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.54 ( 22580 hom., cov: 32)

Exomes 𝑓: 0.53 ( 147824 hom. )

Consequence

EGFR
NM_005228.5 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.900

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=-0.87).

BP6

Variant 7-55151466-C-T is Benign according to our data. Variant chr7-55151466-C-T is described in ClinVar as [Benign]. Clinvar id is 1233950.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.614 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.628+104C>T		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.628+104C>T		intron_variant		1	NM_005228.5	ENSP00000275493.2		P00533-1

Frequencies

GnomAD3 genomes

AF:

0.541

AC:

82212

AN:

151918

Hom.:

22533

Cov.:

show subpopulations

Gnomad AFR

AF:

0.620

Gnomad AMI

AF:

0.521

Gnomad AMR

AF:

0.505

Gnomad ASJ

AF:

0.554

Gnomad EAS

AF:

0.353

Gnomad SAS

AF:

0.557

Gnomad FIN

AF:

0.482

Gnomad MID

AF:

0.456

Gnomad NFE

AF:

0.525

Gnomad OTH

AF:

0.526

GnomAD4 exome

AF:

0.526

AC:

554643

AN:

1054044

Hom.:

147824

AF XY:

0.527

AC XY:

284835

AN XY:

540832

show subpopulations

Gnomad4 AFR exome

AF:

0.623

Gnomad4 AMR exome

AF:

0.531

Gnomad4 ASJ exome

AF:

0.567

Gnomad4 EAS exome

AF:

0.333

Gnomad4 SAS exome

AF:

0.564

Gnomad4 FIN exome

AF:

0.494

Gnomad4 NFE exome

AF:

0.529

Gnomad4 OTH exome

AF:

0.531

GnomAD4 genome

AF:

0.541

AC:

82328

AN:

152038

Hom.:

22580

Cov.:

AF XY:

0.535

AC XY:

39775

AN XY:

74302

show subpopulations

Gnomad4 AFR

AF:

0.620

Gnomad4 AMR

AF:

0.506

Gnomad4 ASJ

AF:

0.554

Gnomad4 EAS

AF:

0.353

Gnomad4 SAS

AF:

0.556

Gnomad4 FIN

AF:

0.482

Gnomad4 NFE

AF:

0.525

Gnomad4 OTH

AF:

0.529

Alfa

AF:

0.512

Hom.:

8646

Bravo

AF:

0.546

Asia WGS

AF:

0.481

AC:

1673

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

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jan 10, 2019	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

1.0

DANN

Benign

0.32

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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