rs7129456

chr11-132652648-G-Achr11-132652648-G-Cchr11-132652648-G-T

Variant summary

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

The NM_001012393.5(OPCML):c.379+4439C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.106 in 152,176 control chromosomes in the GnomAD database, including 1,710 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 0.11 (1710 hom., cov: 33)
• Consequence: OPCML NM_001012393.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.495

Genes affected

OPCML (HGNC:8143): (opioid binding protein/cell adhesion molecule like) This gene encodes a member of the IgLON subfamily in the immunoglobulin protein superfamily of proteins. The encoded preprotein is proteolytically processed to generate the mature protein. This protein is localized in the plasma membrane and may have an accessory role in opioid receptor function. This gene has an ortholog in rat and bovine. The opioid binding-cell adhesion molecule encoded by the rat gene binds opioid alkaloids in the presence of acidic lipids, exhibits selectivity for mu ligands and acts as a GPI-anchored protein. Since the encoded protein is highly conserved in species during evolution, it may have a fundamental role in mammalian systems. Alternative splicing results in multiple transcript variants, at least one of which encodes an isoform that is proteolytically processed. [provided by RefSeq, Jan 2016]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.275 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
OPCML	NM_001012393.5	c.379+4439C>T		intron_variant		ENST00000524381.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
OPCML	ENST00000524381.6	c.379+4439C>T		intron_variant		1	NM_001012393.5

Frequencies

GnomAD3 genomes AF: 0.106 AC: 16171 AN: 152058 Hom.: 1707 Cov.: 33

Gnomad AFR AF: 0.279

Gnomad AMI AF: 0.0439

Gnomad AMR AF: 0.0716

Gnomad ASJ AF: 0.0660

Gnomad EAS AF: 0.000386

Gnomad SAS AF: 0.0550

Gnomad FIN AF: 0.0164

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0390

Gnomad OTH AF: 0.0756

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

GnomAD4 genome AF: 0.106 AC: 16206 AN: 152176 Hom.: 1710 Cov.: 33 AF XY: 0.103 AC XY: 7677 AN XY: 74398

Gnomad4 AFR AF: 0.279

Gnomad4 AMR AF: 0.0713

Gnomad4 ASJ AF: 0.0660

Gnomad4 EAS AF: 0.000387

Gnomad4 SAS AF: 0.0552

Gnomad4 FIN AF: 0.0164

Gnomad4 NFE AF: 0.0390

Gnomad4 OTH AF: 0.0748

Alfa AF: 0.0411 Hom.: 131

Bravo AF: 0.118

Asia WGS AF: 0.0370 AC: 130 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	5.0
Dann	Benign	0.68

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: rs7129456; hg19: chr11-132522543;