11-132835158-A-G

Variant names:

• chr11-132835158-A-G
• rs10791256
• NM_001012393.5:c.146+107768T>C

Variant summary

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

The NM_001012393.5(OPCML):​c.146+107768T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.298 in 152,100 control chromosomes in the GnomAD database, including 7,965 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 0.30 (7965 hom., cov: 32)
• Consequence: OPCML NM_001012393.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.154
• Publications: 2 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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.41 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OPCML	NM_001012393.5	MANE Select	c.146+107768T>C		intron	N/A	NP_001012393.1	Q14982-2
	OPCML	NM_001319103.2		c.167+107768T>C		intron	N/A	NP_001306032.1	Q14982-4
	OPCML	NM_002545.5		c.167+107768T>C		intron	N/A	NP_002536.1	A8K0Y0

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OPCML	ENST00000524381.6	TSL:1 MANE Select	c.146+107768T>C		intron	N/A	ENSP00000434750.1	Q14982-2
	OPCML	ENST00000331898.11	TSL:1	c.167+107768T>C		intron	N/A	ENSP00000330862.7	Q14982-1
	OPCML	ENST00000374778.4	TSL:1	c.44+107768T>C		intron	N/A	ENSP00000363910.4	Q14982-3

Frequencies

GnomAD3 genomes AF: 0.298 AC: 45312 AN: 151982 Hom.: 7964 Cov.: 32

Gnomad AFR AF: 0.152

Gnomad AMI AF: 0.300

Gnomad AMR AF: 0.242

Gnomad ASJ AF: 0.356

Gnomad EAS AF: 0.0344

Gnomad SAS AF: 0.196

Gnomad FIN AF: 0.361

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.414

Gnomad OTH AF: 0.306

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

GnomAD4 genome AF: 0.298 AC: 45317 AN: 152100 Hom.: 7965 Cov.: 32 AF XY: 0.289 AC XY: 21492 AN XY: 74354

African (AFR) AF: 0.151 AC: 6289 AN: 41524

American (AMR) AF: 0.242 AC: 3696 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.356 AC: 1236 AN: 3470

East Asian (EAS) AF: 0.0347 AC: 179 AN: 5156

South Asian (SAS) AF: 0.196 AC: 942 AN: 4818

European-Finnish (FIN) AF: 0.361 AC: 3809 AN: 10562

Middle Eastern (MID) AF: 0.333 AC: 98 AN: 294

European-Non Finnish (NFE) AF: 0.414 AC: 28151 AN: 67972

Other (OTH) AF: 0.305 AC: 643 AN: 2110

Alfa AF: 0.326 Hom.: 1470

Bravo AF: 0.286

Asia WGS AF: 0.109 AC: 382 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.7
DANN	Benign	0.64
PhyloP100		-0.15
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: rs10791256; hg19: chr11-132705053;