Genetic Variant EREG:c.67+152C>T (chr4-74365527-C-T) – ACMG Classification: Likely_benign (-4 pts)

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The NM_001432.3(EREG):c.67+152C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: not found (cov: 17)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

EREG
NM_001432.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.177

Publications

4 publications found

Variant links:

Genes affected

EREG (HGNC:3443): (epiregulin) This gene encodes a secreted peptide hormone and member of the epidermal growth factor (EGF) family of proteins. The encoded protein is a ligand of the epidermal growth factor receptor (EGFR) and the structurally related erb-b2 receptor tyrosine kinase 4 (ERBB4). The encoded protein may be involved in a wide range of biological processes including inflammation, wound healing, oocyte maturation, and cell proliferation. Additionally, the encoded protein may promote the progression of cancers of various human tissues. [provided by RefSeq, Jul 2015]

EREG links:

ENSG00000304732 (HGNC:58817):

ENSG00000304732 links:

LOC105377276 (HGNC:):

LOC105377276 links:

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -4 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.81).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EREG	NM_001432.3 link	c.67+152C>T		intron_variant	Intron 1 of 4	ENST00000244869.3	NP_001423.1
LOC105377276	NR_188415.1 link	n.-186G>A		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein
EREG	ENST00000244869.3 link	c.67+152C>T	intron_variant	Intron 1 of 4	1	NM_001432.3	ENSP00000244869.2
EREG	ENST00000507603.1 link	n.203+152C>T	intron_variant	Intron 1 of 2	2
ENSG00000304732	ENST00000805841.1 link	n.-186G>A	upstream_gene_variant

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

74660

Hom.:

AF XY:

0.00

AC XY:

AN XY:

41684

African (AFR)

AF:

0.00

AC:

AN:

1232

American (AMR)

AF:

0.00

AC:

AN:

2476

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

1820

East Asian (EAS)

AF:

0.00

AC:

AN:

2100

South Asian (SAS)

AF:

0.00

AC:

AN:

15360

European-Finnish (FIN)

AF:

0.00

AC:

AN:

4822

Middle Eastern (MID)

AF:

0.00

AC:

AN:

1130

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

41960

Other (OTH)

AF:

0.00

AC:

AN:

3760

GnomAD4 genome

Cov.:

Alfa

AF:

0.00

Hom.:

2350

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

5.2

(source)

DANN

Benign

0.96

PhyloP100

-0.18

PromoterAI

0.060

Neutral

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over