ENST00000578199.5:c.-277+1459A>T

Variant names:

• chr17-39690259-A-T
• rs2517959
• ENST00000578199.5:c.-277+1459A>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000578199.5(ERBB2):​c.-277+1459A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.622 in 151,416 control chromosomes in the GnomAD database, including 29,760 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 0.62 (29760 hom., cov: 30)
• Consequence: ERBB2 ENST00000578199.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.876
• Publications: 15 publications found

Genes affected

ERBB2 (HGNC:3430): (erb-b2 receptor tyrosine kinase 2) This gene encodes a member of the epidermal growth factor (EGF) receptor family of receptor tyrosine kinases. This protein has no ligand binding domain of its own and therefore cannot bind growth factors. However, it does bind tightly to other ligand-bound EGF receptor family members to form a heterodimer, stabilizing ligand binding and enhancing kinase-mediated activation of downstream signalling pathways, such as those involving mitogen-activated protein kinase and phosphatidylinositol-3 kinase. Allelic variations at amino acid positions 654 and 655 of isoform a (positions 624 and 625 of isoform b) have been reported, with the most common allele, Ile654/Ile655, shown here. Amplification and/or overexpression of this gene has been reported in numerous cancers, including breast and ovarian tumors. Alternative splicing results in several additional transcript variants, some encoding different isoforms and others that have not been fully characterized. [provided by RefSeq, Jul 2008]

PGAP3 (HGNC:23719): (post-GPI attachment to proteins phospholipase 3) This gene encodes a glycosylphosphatidylinositol (GPI)-specific phospholipase that primarily localizes to the Golgi apparatus. This ubiquitously expressed gene is predicted to encode a seven-transmembrane protein that removes unsaturated fatty acids from the sn-2 position of GPI. The remodeling of the constituent fatty acids on GPI is thought to be important for the proper association between GPI-anchored proteins and lipid rafts. The tethering of proteins to plasma membranes via posttranslational GPI-anchoring is thought to play a role in protein sorting and trafficking. Mutations in this gene cause an autosomal recessive form of neurologic hyperphosphatasia with cognitive disability (HPMRS4). Alternative splicing results in multiple transcript variants encoding distinct isoforms. [provided by RefSeq, Jul 2017]

PGAP3 Gene-Disease associations (from GenCC):

• hyperphosphatasia with intellectual disability syndrome 4

  Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: G2P, ClinGen, Labcorp Genetics (formerly Invitae)
• hyperphosphatasia-intellectual disability syndrome

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.711 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ERBB2	NM_001289936.2	c.-283+1459A>T		intron_variant	Intron 2 of 30		NP_001276865.1
ERBB2	NM_001005862.3	c.-277+1459A>T		intron_variant	Intron 2 of 29		NP_001005862.1
ERBB2	NM_001382782.1	c.-584+1459A>T		intron_variant	Intron 2 of 29		NP_001369711.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ERBB2	ENST00000578199.5	c.-277+1459A>T		intron_variant	Intron 2 of 17	1		ENSP00000462808.1
ERBB2	ENST00000584014.5	n.283+1459A>T		intron_variant	Intron 2 of 3	1
ERBB2	ENST00000584601.5	c.-328+1459A>T		intron_variant	Intron 2 of 30	2		ENSP00000462438.1
PGAP3	ENST00000584856.1	c.-35-4240T>A		intron_variant	Intron 1 of 2	4		ENSP00000463785.1

Frequencies

GnomAD3 genomes AF: 0.622 AC: 94145 AN: 151298 Hom.: 29727 Cov.: 30

Gnomad AFR AF: 0.545

Gnomad AMI AF: 0.738

Gnomad AMR AF: 0.584

Gnomad ASJ AF: 0.696

Gnomad EAS AF: 0.400

Gnomad SAS AF: 0.731

Gnomad FIN AF: 0.701

Gnomad MID AF: 0.701

Gnomad NFE AF: 0.670

Gnomad OTH AF: 0.619

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

GnomAD4 genome AF: 0.622 AC: 94240 AN: 151416 Hom.: 29760 Cov.: 30 AF XY: 0.622 AC XY: 45978 AN XY: 73962

African (AFR) AF: 0.545 AC: 22529 AN: 41330

American (AMR) AF: 0.584 AC: 8903 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.696 AC: 2408 AN: 3458

East Asian (EAS) AF: 0.400 AC: 2051 AN: 5130

South Asian (SAS) AF: 0.732 AC: 3512 AN: 4800

European-Finnish (FIN) AF: 0.701 AC: 7322 AN: 10446

Middle Eastern (MID) AF: 0.688 AC: 201 AN: 292

European-Non Finnish (NFE) AF: 0.670 AC: 45338 AN: 67716

Other (OTH) AF: 0.621 AC: 1307 AN: 2106

Alfa AF: 0.641 Hom.: 3815

Bravo AF: 0.607

Asia WGS AF: 0.626 AC: 2179 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.042
DANN	Benign	0.17
PhyloP100		-0.88
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs2517959; hg19: chr17-37846512; COSMIC: COSV56131593; COSMIC: COSV56131593;