rs13387495

chr2-212420333-T-Cchr2-212420333-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_005235.3(ERBB4):c.82+118116A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0927 in 152,080 control chromosomes in the GnomAD database, including 895 homozygotes. 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: 𝑓 0.093 (895 hom., cov: 32)
• Consequence: ERBB4 NM_005235.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.750

Genes affected

ERBB4 (HGNC:3432): (erb-b2 receptor tyrosine kinase 4) This gene is a member of the Tyr protein kinase family and the epidermal growth factor receptor subfamily. It encodes a single-pass type I membrane protein with multiple cysteine rich domains, a transmembrane domain, a tyrosine kinase domain, a phosphotidylinositol-3 kinase binding site and a PDZ domain binding motif. The protein binds to and is activated by neuregulins and other factors and induces a variety of cellular responses including mitogenesis and differentiation. Multiple proteolytic events allow for the release of a cytoplasmic fragment and an extracellular fragment. Mutations in this gene have been associated with cancer. Alternatively spliced variants which encode different protein isoforms have been described; however, not all variants have been fully characterized. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.144 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ERBB4	NM_005235.3	c.82+118116A>G		intron_variant		ENST00000342788.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ERBB4	ENST00000342788.9	c.82+118116A>G		intron_variant		1	NM_005235.3	P4

Frequencies

GnomAD3 genomes AF: 0.0927 AC: 14092 AN: 151962 Hom.: 893 Cov.: 32

Gnomad AFR AF: 0.0260

Gnomad AMI AF: 0.111

Gnomad AMR AF: 0.0696

Gnomad ASJ AF: 0.123

Gnomad EAS AF: 0.00231

Gnomad SAS AF: 0.0929

Gnomad FIN AF: 0.0801

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.146

Gnomad OTH AF: 0.0876

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0927 AC: 14099 AN: 152080 Hom.: 895 Cov.: 32 AF XY: 0.0887 AC XY: 6599 AN XY: 74358

Gnomad4 AFR AF: 0.0260

Gnomad4 AMR AF: 0.0694

Gnomad4 ASJ AF: 0.123

Gnomad4 EAS AF: 0.00231

Gnomad4 SAS AF: 0.0944

Gnomad4 FIN AF: 0.0801

Gnomad4 NFE AF: 0.146

Gnomad4 OTH AF: 0.0867

Alfa AF: 0.131 Hom.: 1686

Bravo AF: 0.0879

Asia WGS AF: 0.0370 AC: 128 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	4.9
Dann	Benign	0.57

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: rs13387495; hg19: chr2-213285057;