chr11-132656970-A-G

Variant names:

• chr11-132656970-A-G
• rs1784519
• NM_001012393.5:c.379+117T>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.379+117T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.768 in 1,482,142 control chromosomes in the GnomAD database, including 439,289 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 0.81 (50026 hom., cov: 33)
  • Exomes 𝑓: 0.76 (389263 hom.)
• Consequence: OPCML NM_001012393.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.458
• Publications: 6 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 (AFR) allele frequency at 95% confidence interval = 0.932 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.379+117T>C		intron	N/A	NP_001012393.1	Q14982-2
	OPCML	NM_001319103.2		c.400+117T>C		intron	N/A	NP_001306032.1	Q14982-4
	OPCML	NM_002545.5		c.400+117T>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.379+117T>C		intron	N/A	ENSP00000434750.1	Q14982-2
	OPCML	ENST00000331898.11	TSL:1	c.400+117T>C		intron	N/A	ENSP00000330862.7	Q14982-1
	OPCML	ENST00000374778.4	TSL:1	c.277+117T>C		intron	N/A	ENSP00000363910.4	Q14982-3

Frequencies

GnomAD3 genomes AF: 0.805 AC: 122453 AN: 152106 Hom.: 49971 Cov.: 33

Gnomad AFR AF: 0.940

Gnomad AMI AF: 0.698

Gnomad AMR AF: 0.763

Gnomad ASJ AF: 0.725

Gnomad EAS AF: 0.581

Gnomad SAS AF: 0.749

Gnomad FIN AF: 0.766

Gnomad MID AF: 0.758

Gnomad NFE AF: 0.767

Gnomad OTH AF: 0.761

GnomAD4 exome AF: 0.764 AC: 1015892 AN: 1329920 Hom.: 389263 AF XY: 0.763 AC XY: 493889 AN XY: 647716

African (AFR) AF: 0.948 AC: 28485 AN: 30040

American (AMR) AF: 0.737 AC: 20467 AN: 27786

Ashkenazi Jewish (ASJ) AF: 0.732 AC: 14713 AN: 20088

East Asian (EAS) AF: 0.599 AC: 22064 AN: 36812

South Asian (SAS) AF: 0.758 AC: 51231 AN: 67554

European-Finnish (FIN) AF: 0.755 AC: 36093 AN: 47798

Middle Eastern (MID) AF: 0.745 AC: 2810 AN: 3770

European-Non Finnish (NFE) AF: 0.767 AC: 798458 AN: 1041224

Other (OTH) AF: 0.758 AC: 41571 AN: 54848

GnomAD4 genome AF: 0.805 AC: 122562 AN: 152222 Hom.: 50026 Cov.: 33 AF XY: 0.802 AC XY: 59699 AN XY: 74412

African (AFR) AF: 0.940 AC: 39072 AN: 41566

American (AMR) AF: 0.762 AC: 11664 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.725 AC: 2517 AN: 3470

East Asian (EAS) AF: 0.580 AC: 2998 AN: 5172

South Asian (SAS) AF: 0.750 AC: 3615 AN: 4820

European-Finnish (FIN) AF: 0.766 AC: 8112 AN: 10584

Middle Eastern (MID) AF: 0.771 AC: 225 AN: 292

European-Non Finnish (NFE) AF: 0.767 AC: 52125 AN: 68000

Other (OTH) AF: 0.758 AC: 1599 AN: 2110

Alfa AF: 0.785 Hom.: 7362

Bravo AF: 0.805

Asia WGS AF: 0.696 AC: 2422 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	0.80
DANN	Benign	0.37
PhyloP100		-0.46
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: rs1784519; hg19: chr11-132526865;