11-132714224-C-T

Variant names:

• chr11-132714224-C-T
• rs1793257
• NM_001012393.5:c.147-56905G>A

Variant summary

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

The NM_001012393.5(OPCML):​c.147-56905G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0733 in 152,222 control chromosomes in the GnomAD database, including 690 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 0.073 (690 hom., cov: 33)
• Consequence: OPCML NM_001012393.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.388
• Publications: 5 publications found

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

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.158 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001012393.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OPCML	NM_001012393.5	MANE Select	c.147-56905G>A		intron	N/A	NP_001012393.1
	OPCML	NM_001319103.2		c.168-56905G>A		intron	N/A	NP_001306032.1
	OPCML	NM_002545.5		c.168-56905G>A		intron	N/A	NP_002536.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OPCML	ENST00000524381.6	TSL:1 MANE Select	c.147-56905G>A		intron	N/A	ENSP00000434750.1
	OPCML	ENST00000331898.11	TSL:1	c.168-56905G>A		intron	N/A	ENSP00000330862.7
	OPCML	ENST00000374778.4	TSL:1	c.45-56905G>A		intron	N/A	ENSP00000363910.4

Frequencies

GnomAD3 genomes AF: 0.0732 AC: 11134 AN: 152104 Hom.: 687 Cov.: 33

Gnomad AFR AF: 0.161

Gnomad AMI AF: 0.0373

Gnomad AMR AF: 0.0407

Gnomad ASJ AF: 0.0305

Gnomad EAS AF: 0.0524

Gnomad SAS AF: 0.0729

Gnomad FIN AF: 0.0354

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0379

Gnomad OTH AF: 0.0522

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

GnomAD4 genome AF: 0.0733 AC: 11158 AN: 152222 Hom.: 690 Cov.: 33 AF XY: 0.0735 AC XY: 5473 AN XY: 74416

African (AFR) AF: 0.161 AC: 6690 AN: 41510

American (AMR) AF: 0.0405 AC: 619 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0305 AC: 106 AN: 3472

East Asian (EAS) AF: 0.0521 AC: 270 AN: 5178

South Asian (SAS) AF: 0.0740 AC: 357 AN: 4824

European-Finnish (FIN) AF: 0.0354 AC: 376 AN: 10610

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.0379 AC: 2578 AN: 68020

Other (OTH) AF: 0.0517 AC: 109 AN: 2110

Alfa AF: 0.0501 Hom.: 649

Bravo AF: 0.0769

Asia WGS AF: 0.0560 AC: 194 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.3
DANN	Benign	0.29
PhyloP100		-0.39
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

Other links and lift over

dbSNP: rs1793257; hg19: chr11-132584119;