5-65932423-G-C

Variant summary

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

The NM_001253697.2(ERBIN):c.-58+5617G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.701 in 151,908 control chromosomes in the GnomAD database, including 39,626 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 0.70 (39626 hom., cov: 31)
• Consequence: ERBIN NM_001253697.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.166

Genes affected

ERBIN (HGNC:15842): (erbb2 interacting protein) This gene is a member of the leucine-rich repeat and PDZ domain (LAP) family. The encoded protein contains 17 leucine-rich repeats and one PDZ domain. It binds to the unphosphorylated form of the ERBB2 protein and regulates ERBB2 function and localization. It has also been shown to affect the Ras signaling pathway by disrupting Ras-Raf interaction. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Nov 2011]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.837 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ERBIN	NM_001253697.2	c.-58+5617G>C		intron_variant		ENST00000284037.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ERBIN	ENST00000284037.10	c.-58+5617G>C		intron_variant		1	NM_001253697.2	A1

Frequencies

GnomAD3 genomes AF: 0.702 AC: 106542 AN: 151808 Hom.: 39621 Cov.: 31

Gnomad AFR AF: 0.461

Gnomad AMI AF: 0.810

Gnomad AMR AF: 0.637

Gnomad ASJ AF: 0.713

Gnomad EAS AF: 0.533

Gnomad SAS AF: 0.822

Gnomad FIN AF: 0.842

Gnomad MID AF: 0.715

Gnomad NFE AF: 0.843

Gnomad OTH AF: 0.707

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

GnomAD4 genome AF: 0.701 AC: 106558 AN: 151908 Hom.: 39626 Cov.: 31 AF XY: 0.700 AC XY: 51954 AN XY: 74226

Gnomad4 AFR AF: 0.461

Gnomad4 AMR AF: 0.636

Gnomad4 ASJ AF: 0.713

Gnomad4 EAS AF: 0.534

Gnomad4 SAS AF: 0.823

Gnomad4 FIN AF: 0.842

Gnomad4 NFE AF: 0.843

Gnomad4 OTH AF: 0.708

Alfa AF: 0.681 Hom.: 2319

Bravo AF: 0.671

Asia WGS AF: 0.710 AC: 2472 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	2.5
Dann	Benign	0.54

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: rs251614; hg19: chr5-65228251;