chr11-133418524-G-A

Variant names:

• chr11-133418524-G-A
• rs1941211
• NM_001012393.5:c.61+113740C>T

Variant summary

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

The NM_001012393.5(OPCML):​c.61+113740C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0183 in 938,608 control chromosomes in the GnomAD database, including 1,560 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 0.071 (1090 hom., cov: 32)
  • Exomes 𝑓: 0.0082 (470 hom.)
• Consequence: OPCML NM_001012393.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.618
• Publications: 1 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=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.218 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.61+113740C>T		intron	N/A	NP_001012393.1
	OPCML	NM_001319104.4		c.-134+113740C>T		intron	N/A	NP_001306033.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OPCML	ENST00000524381.6	TSL:1 MANE Select	c.61+113740C>T		intron	N/A	ENSP00000434750.1
	OPCML	ENST00000529038.5	TSL:5	n.139+113740C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0705 AC: 10718 AN: 152094 Hom.: 1077 Cov.: 32

Gnomad AFR AF: 0.222

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0327

Gnomad ASJ AF: 0.0176

Gnomad EAS AF: 0.0632

Gnomad SAS AF: 0.0247

Gnomad FIN AF: 0.0121

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.00432

Gnomad OTH AF: 0.0512

GnomAD4 exome AF: 0.00818 AC: 6433 AN: 786396 Hom.: 470 Cov.: 13 AF XY: 0.00789 AC XY: 2878 AN XY: 364744

African (AFR) AF: 0.250 AC: 3677 AN: 14690

American (AMR) AF: 0.0350 AC: 33 AN: 942

Ashkenazi Jewish (ASJ) AF: 0.0148 AC: 72 AN: 4850

East Asian (EAS) AF: 0.0546 AC: 184 AN: 3368

South Asian (SAS) AF: 0.0241 AC: 375 AN: 15576

European-Finnish (FIN) AF: 0.0113 AC: 3 AN: 266

Middle Eastern (MID) AF: 0.0338 AC: 52 AN: 1538

European-Non Finnish (NFE) AF: 0.00211 AC: 1519 AN: 719414

Other (OTH) AF: 0.0201 AC: 518 AN: 25752

GnomAD4 genome AF: 0.0708 AC: 10774 AN: 152212 Hom.: 1090 Cov.: 32 AF XY: 0.0697 AC XY: 5189 AN XY: 74442

African (AFR) AF: 0.222 AC: 9223 AN: 41494

American (AMR) AF: 0.0326 AC: 499 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0176 AC: 61 AN: 3470

East Asian (EAS) AF: 0.0635 AC: 329 AN: 5178

South Asian (SAS) AF: 0.0249 AC: 120 AN: 4820

European-Finnish (FIN) AF: 0.0121 AC: 128 AN: 10614

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.00432 AC: 294 AN: 68026

Other (OTH) AF: 0.0507 AC: 107 AN: 2112

Alfa AF: 0.0531 Hom.: 129

Bravo AF: 0.0786

Asia WGS AF: 0.0520 AC: 180 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	4.8
DANN	Benign	0.76
PhyloP100		0.62
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1941211; hg19: chr11-133288419;