chr5-65932423-G-C

Variant names:

• chr5-65932423-G-C
• rs251614
• NM_001253697.2:c.-58+5617G>C

Variant summary

Our verdict is Benign. The variant received -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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
ERBIN	NM_001253697.2	c.-58+5617G>C		intron_variant	Intron 1 of 25	ENST00000284037.10	NP_001240626.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ERBIN	ENST00000284037.10	c.-58+5617G>C		intron_variant	Intron 1 of 25	1	NM_001253697.2	ENSP00000284037.4

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

African (AFR) AF: 0.461 AC: 19054 AN: 41366

American (AMR) AF: 0.636 AC: 9720 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.713 AC: 2469 AN: 3464

East Asian (EAS) AF: 0.534 AC: 2742 AN: 5138

South Asian (SAS) AF: 0.823 AC: 3965 AN: 4818

European-Finnish (FIN) AF: 0.842 AC: 8876 AN: 10540

Middle Eastern (MID) AF: 0.718 AC: 211 AN: 294

European-Non Finnish (NFE) AF: 0.843 AC: 57292 AN: 67994

Other (OTH) AF: 0.708 AC: 1490 AN: 2106

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
PhyloP100		-0.17
Mutation Taster		=100/0	polymorphism (auto)

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

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Other links and lift over

dbSNP: rs251614; hg19: chr5-65228251;