chr11-132427310-G-A

Variant names:

• chr11-132427310-G-A
• rs1939966
• NM_001012393.5:c.917-7017C>T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_001012393.5(OPCML):​c.917-7017C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.282 in 152,124 control chromosomes in the GnomAD database, including 6,240 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 0.28 (6240 hom., cov: 33)
• Consequence: OPCML NM_001012393.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.86
• Publications: 3 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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.37).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.306 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.917-7017C>T		intron	N/A	NP_001012393.1
	OPCML	NM_001319103.2		c.965-7017C>T		intron	N/A	NP_001306032.1
	OPCML	NM_002545.5		c.938-7017C>T		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.917-7017C>T		intron	N/A	ENSP00000434750.1
	OPCML	ENST00000331898.11	TSL:1	c.938-7017C>T		intron	N/A	ENSP00000330862.7
	OPCML	ENST00000374778.4	TSL:1	c.815-7017C>T		intron	N/A	ENSP00000363910.4

Frequencies

GnomAD3 genomes AF: 0.283 AC: 42949 AN: 152002 Hom.: 6234 Cov.: 33

Gnomad AFR AF: 0.229

Gnomad AMI AF: 0.152

Gnomad AMR AF: 0.306

Gnomad ASJ AF: 0.192

Gnomad EAS AF: 0.213

Gnomad SAS AF: 0.225

Gnomad FIN AF: 0.395

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.310

Gnomad OTH AF: 0.248

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

GnomAD4 genome AF: 0.282 AC: 42966 AN: 152124 Hom.: 6240 Cov.: 33 AF XY: 0.285 AC XY: 21178 AN XY: 74358

African (AFR) AF: 0.229 AC: 9488 AN: 41510

American (AMR) AF: 0.307 AC: 4686 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.192 AC: 665 AN: 3470

East Asian (EAS) AF: 0.213 AC: 1099 AN: 5162

South Asian (SAS) AF: 0.225 AC: 1082 AN: 4816

European-Finnish (FIN) AF: 0.395 AC: 4180 AN: 10578

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.310 AC: 21071 AN: 67984

Other (OTH) AF: 0.247 AC: 523 AN: 2114

Alfa AF: 0.287 Hom.: 8355

Bravo AF: 0.269

Asia WGS AF: 0.225 AC: 781 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.37
CADD	Benign	16
DANN	Benign	0.71
PhyloP100		1.9
Mutation Taster		=92/8	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: rs1939966; hg19: chr11-132297204;