chr11-132656970-A-G

Position:

• chr11-132656970-A-G

Variant summary

Our verdict is Benign. Variant got -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

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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.932 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OPCML	NM_001012393.5	c.379+117T>C		intron_variant		ENST00000524381.6	NP_001012393.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OPCML	ENST00000524381.6	c.379+117T>C		intron_variant		1	NM_001012393.5	ENSP00000434750

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

Gnomad4 AFR exome AF: 0.948

Gnomad4 AMR exome AF: 0.737

Gnomad4 ASJ exome AF: 0.732

Gnomad4 EAS exome AF: 0.599

Gnomad4 SAS exome AF: 0.758

Gnomad4 FIN exome AF: 0.755

Gnomad4 NFE exome AF: 0.767

Gnomad4 OTH exome AF: 0.758

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

Gnomad4 AFR AF: 0.940

Gnomad4 AMR AF: 0.762

Gnomad4 ASJ AF: 0.725

Gnomad4 EAS AF: 0.580

Gnomad4 SAS AF: 0.750

Gnomad4 FIN AF: 0.766

Gnomad4 NFE AF: 0.767

Gnomad4 OTH AF: 0.758

Alfa AF: 0.780 Hom.: 7031

Bravo AF: 0.805

Asia WGS AF: 0.696 AC: 2422 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.80
DANN	Benign	0.37

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: rs1784519; hg19: chr11-132526865;