dbSNP rs1941212: OPCML:c.61+113824A>G (chr11-133418440-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001012393.5(OPCML):c.61+113824A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.018 in 985,222 control chromosomes in the GnomAD database, including 1,600 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 ( 1087 hom., cov: 32)

Exomes 𝑓: 0.0083 ( 513 hom. )

Consequence

OPCML
NM_001012393.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.976

Publications

2 publications found

Variant links:

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]

OPCML links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.82).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.218 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
OPCML	NM_001012393.5 link	c.61+113824A>G	intron_variant	Intron 1 of 7	ENST00000524381.6	NP_001012393.1	Q14982-2
OPCML	NM_001319104.4 link	c.-134+113824A>G	intron_variant	Intron 1 of 6		NP_001306033.1	Q14982B2CZX3
OPCML	XM_006718846.4 link	c.61+113824A>G	intron_variant	Intron 1 of 7		XP_006718909.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OPCML	ENST00000524381.6 link	c.61+113824A>G		intron_variant	Intron 1 of 7	1	NM_001012393.5	ENSP00000434750.1		Q14982-2
OPCML	ENST00000529038.5 link	n.139+113824A>G		intron_variant	Intron 1 of 6	5

Frequencies

GnomAD3 genomes

AF:

0.0705

AC:

10717

AN:

152084

Hom.:

1074

Cov.:

show subpopulations

Gnomad AFR

AF:

0.221

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0328

Gnomad ASJ

AF:

0.0176

Gnomad EAS

AF:

0.0633

Gnomad SAS

AF:

0.0251

Gnomad FIN

AF:

0.0120

Gnomad MID

AF:

0.0380

Gnomad NFE

AF:

0.00432

Gnomad OTH

AF:

0.0512

GnomAD4 exome

AF:

0.00834

AC:

6946

AN:

833020

Hom.:

513

Cov.:

AF XY:

0.00802

AC XY:

3086

AN XY:

384684

show subpopulations

African (AFR)

AF:

0.252

AC:

3975

AN:

15766

American (AMR)

AF:

0.0356

AC:

AN:

984

Ashkenazi Jewish (ASJ)

AF:

0.0150

AC:

AN:

5150

East Asian (EAS)

AF:

0.0584

AC:

212

AN:

3630

South Asian (SAS)

AF:

0.0240

AC:

395

AN:

16460

European-Finnish (FIN)

AF:

0.0109

AC:

AN:

276

Middle Eastern (MID)

AF:

0.0340

AC:

AN:

1620

European-Non Finnish (NFE)

AF:

0.00214

AC:

1631

AN:

761842

Other (OTH)

AF:

0.0206

AC:

563

AN:

27292

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.457

Heterozygous variant carriers

270

541

811

1082

1352

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

268

536

804

1072

1340

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0708

AC:

10773

AN:

152202

Hom.:

1087

Cov.:

AF XY:

0.0697

AC XY:

5188

AN XY:

74432

show subpopulations

African (AFR)

AF:

0.222

AC:

9217

AN:

41504

American (AMR)

AF:

0.0327

AC:

501

AN:

15298

Ashkenazi Jewish (ASJ)

AF:

0.0176

AC:

AN:

3468

East Asian (EAS)

AF:

0.0637

AC:

330

AN:

5182

South Asian (SAS)

AF:

0.0254

AC:

122

AN:

4812

European-Finnish (FIN)

AF:

0.0120

AC:

128

AN:

10624

Middle Eastern (MID)

AF:

0.0442

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00432

AC:

294

AN:

67998

Other (OTH)

AF:

0.0507

AC:

107

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

448

896

1344

1792

2240

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

196

294

392

490

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0435

Hom.:

348

Bravo

AF:

0.0786

Asia WGS

AF:

0.0520

AC:

180

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

(source)

DANN

Benign

0.85

PhyloP100

0.98

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over