Variant chr7-55170575-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 ENST00000344576.7(EGFR):c.*31G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.347 in 1,610,342 control chromosomes in the GnomAD database, including 100,669 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.32 ( 8535 hom., cov: 32)

Exomes 𝑓: 0.35 ( 92134 hom. )

Consequence

EGFR
ENST00000344576.7 3_prime_UTR

Scores

Clinical Significance

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

Conservation

PhyloP100: -3.22

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.97).

BP6

Variant 7-55170575-G-A is Benign according to our data. Variant chr7-55170575-G-A is described in ClinVar as [Benign]. Clinvar id is 1289672.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.535 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
EGFR	NM_005228.5 linkuse as main transcript	c.1881-600G>A		intron_variant		ENST00000275493.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
EGFR	ENST00000275493.7 linkuse as main transcript	c.1881-600G>A		intron_variant		1	NM_005228.5	P1	P00533-1

Frequencies

GnomAD3 genomes

AF:

0.325

AC:

49272

AN:

151754

Hom.:

8538

Cov.:

show subpopulations

Gnomad AFR

AF:

0.232

Gnomad AMI

AF:

0.357

Gnomad AMR

AF:

0.362

Gnomad ASJ

AF:

0.476

Gnomad EAS

AF:

0.551

Gnomad SAS

AF:

0.439

Gnomad FIN

AF:

0.313

Gnomad MID

AF:

0.449

Gnomad NFE

AF:

0.339

Gnomad OTH

AF:

0.358

GnomAD3 exomes

AF:

0.371

AC:

92479

AN:

249574

Hom.:

17864

AF XY:

0.375

AC XY:

50635

AN XY:

135102

show subpopulations

Gnomad AFR exome

AF:

0.229

Gnomad AMR exome

AF:

0.391

Gnomad ASJ exome

AF:

0.483

Gnomad EAS exome

AF:

0.539

Gnomad SAS exome

AF:

0.422

Gnomad FIN exome

AF:

0.313

Gnomad NFE exome

AF:

0.343

Gnomad OTH exome

AF:

0.390

GnomAD4 exome

AF:

0.350

AC:

510302

AN:

1458470

Hom.:

92134

Cov.:

AF XY:

0.353

AC XY:

256083

AN XY:

725752

show subpopulations

Gnomad4 AFR exome

AF:

0.226

Gnomad4 AMR exome

AF:

0.389

Gnomad4 ASJ exome

AF:

0.488

Gnomad4 EAS exome

AF:

0.603

Gnomad4 SAS exome

AF:

0.424

Gnomad4 FIN exome

AF:

0.312

Gnomad4 NFE exome

AF:

0.334

Gnomad4 OTH exome

AF:

0.374

GnomAD4 genome

AF:

0.324

AC:

49277

AN:

151872

Hom.:

8535

Cov.:

AF XY:

0.329

AC XY:

24407

AN XY:

74234

show subpopulations

Gnomad4 AFR

AF:

0.231

Gnomad4 AMR

AF:

0.361

Gnomad4 ASJ

AF:

0.476

Gnomad4 EAS

AF:

0.552

Gnomad4 SAS

AF:

0.439

Gnomad4 FIN

AF:

0.313

Gnomad4 NFE

AF:

0.339

Gnomad4 OTH

AF:

0.359

Alfa

AF:

0.352

Hom.:

17016

Bravo

AF:

0.328

Asia WGS

AF:

0.475

AC:

1649

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	Feb 07, 2019	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.97

CADD

Benign

0.078

DANN

Benign

0.51

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