12-56084874-A-C

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_001982.4(ERBB3):c.235-121A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.58 in 1,485,504 control chromosomes in the GnomAD database, including 257,414 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.52 (22372 hom., cov: 30)
  • Exomes 𝑓: 0.59 (235042 hom.)
• Consequence: ERBB3 NM_001982.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.09

Genes affected

ERBB3 (HGNC:3431): (erb-b2 receptor tyrosine kinase 3) This gene encodes a member of the epidermal growth factor receptor (EGFR) family of receptor tyrosine kinases. This membrane-bound protein has a neuregulin binding domain but not an active kinase domain. It therefore can bind this ligand but not convey the signal into the cell through protein phosphorylation. However, it does form heterodimers with other EGF receptor family members which do have kinase activity. Heterodimerization leads to the activation of pathways which lead to cell proliferation or differentiation. Amplification of this gene and/or overexpression of its protein have been reported in numerous cancers, including prostate, bladder, and breast tumors. Alternate transcriptional splice variants encoding different isoforms have been characterized. One isoform lacks the intermembrane region and is secreted outside the cell. This form acts to modulate the activity of the membrane-bound form. Additional splice variants have also been reported, but they have not been thoroughly characterized. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BP6: Variant 12-56084874-A-C is Benign according to our data. Variant chr12-56084874-A-C is described in ClinVar as [Benign]. Clinvar id is 1221690.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.753 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ERBB3	NM_001982.4	c.235-121A>C		intron_variant		ENST00000267101.8
ERBB3	NM_001005915.1	c.235-121A>C		intron_variant
ERBB3	XM_047428500.1	c.58-121A>C		intron_variant
ERBB3	XM_047428501.1	c.58-121A>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ERBB3	ENST00000267101.8	c.235-121A>C		intron_variant		1	NM_001982.4	P1

Frequencies

GnomAD3 genomes AF: 0.516 AC: 78302 AN: 151882 Hom.: 22356 Cov.: 30

Gnomad AFR AF: 0.257

Gnomad AMI AF: 0.419

Gnomad AMR AF: 0.654

Gnomad ASJ AF: 0.542

Gnomad EAS AF: 0.772

Gnomad SAS AF: 0.720

Gnomad FIN AF: 0.620

Gnomad MID AF: 0.680

Gnomad NFE AF: 0.589

Gnomad OTH AF: 0.564

GnomAD4 exome AF: 0.588 AC: 783738 AN: 1333504 Hom.: 235042 AF XY: 0.593 AC XY: 392273 AN XY: 661812

Gnomad4 AFR exome AF: 0.248

Gnomad4 AMR exome AF: 0.742

Gnomad4 ASJ exome AF: 0.552

Gnomad4 EAS exome AF: 0.789

Gnomad4 SAS exome AF: 0.714

Gnomad4 FIN exome AF: 0.594

Gnomad4 NFE exome AF: 0.576

Gnomad4 OTH exome AF: 0.589

GnomAD4 genome AF: 0.515 AC: 78349 AN: 152000 Hom.: 22372 Cov.: 30 AF XY: 0.526 AC XY: 39063 AN XY: 74294

Gnomad4 AFR AF: 0.258

Gnomad4 AMR AF: 0.654

Gnomad4 ASJ AF: 0.542

Gnomad4 EAS AF: 0.773

Gnomad4 SAS AF: 0.720

Gnomad4 FIN AF: 0.620

Gnomad4 NFE AF: 0.589

Gnomad4 OTH AF: 0.565

Alfa AF: 0.565 Hom.: 4678

Bravo AF: 0.505

Asia WGS AF: 0.740 AC: 2569 AN: 3476

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Sep 04, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	5.7
Dann	Benign	0.60

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

Other links and lift over

dbSNP: rs7971751; hg19: chr12-56478658;