Variant 11-77102915-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_006189.1(OMP):c.76C>T(p.Arg26Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0551 in 1,612,714 control chromosomes in the GnomAD database, including 3,369 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. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R26L) has been classified as Uncertain significance.

Frequency

Genomes: 𝑓 0.053 ( 409 hom., cov: 33)

Exomes 𝑓: 0.055 ( 2960 hom. )

Consequence

OMP
NM_006189.1 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.39

Variant links:

Genes affected

OMP (HGNC:8136): (olfactory marker protein) Olfactory marker protein is uniquely associated with the mature olfactory receptor neurons in many vertebrate species from fish to man. The OMP gene structure and protein sequence are highly conserved between mouse, rat and human. Results of the mouse knockout studies show that OMP-null mice are compromised in their ability to respond to odor stimuli, and that OMP represents a novel modulatory component of the odor detection/signal transduction cascade. [provided by RefSeq, Jul 2008]

OMP links:

CAPN5 (HGNC:1482): (calpain 5) Calpains are calcium-dependent cysteine proteases involved in signal transduction in a variety of cellular processes. A functional calpain protein consists of an invariant small subunit and 1 of a family of large subunits. CAPN5 is one of the large subunits. Unlike some of the calpains, CAPN5 and CAPN6 lack a calmodulin-like domain IV. Because of the significant similarity to Caenorhabditis elegans sex determination gene tra-3, CAPN5 is also called as HTRA3. [provided by RefSeq, Jul 2008]

CAPN5 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0025221407).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.147 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
OMP	NM_006189.1 linkuse as main transcript	c.76C>T	p.Arg26Trp	missense_variant	1/1	ENST00000529803.1
CAPN5	NM_004055.5 linkuse as main transcript	c.297+9102C>T		intron_variant		ENST00000648180.1
CAPN5	XM_011545225.1 linkuse as main transcript	c.417+9102C>T		intron_variant
CAPN5	XM_017018223.3 linkuse as main transcript	c.405+9102C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
OMP	ENST00000529803.1 linkuse as main transcript	c.76C>T	p.Arg26Trp	missense_variant	1/1		NM_006189.1	P1
CAPN5	ENST00000648180.1 linkuse as main transcript	c.297+9102C>T		intron_variant			NM_004055.5	P1

Frequencies

GnomAD3 genomes

AF:

0.0528

AC:

8038

AN:

152234

Hom.:

410

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0112

Gnomad AMI

AF:

0.0614

Gnomad AMR

AF:

0.152

Gnomad ASJ

AF:

0.0317

Gnomad EAS

AF:

0.00192

Gnomad SAS

AF:

0.0205

Gnomad FIN

AF:

0.110

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.0541

Gnomad OTH

AF:

0.0573

GnomAD3 exomes

AF:

0.0699

AC:

17180

AN:

245804

Hom.:

1064

AF XY:

0.0623

AC XY:

8354

AN XY:

134142

show subpopulations

Gnomad AFR exome

AF:

0.0105

Gnomad AMR exome

AF:

0.208

Gnomad ASJ exome

AF:

0.0321

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.0205

Gnomad FIN exome

AF:

0.113

Gnomad NFE exome

AF:

0.0551

Gnomad OTH exome

AF:

0.0668

GnomAD4 exome

AF:

0.0553

AC:

80789

AN:

1460362

Hom.:

2960

Cov.:

AF XY:

0.0533

AC XY:

38707

AN XY:

726488

show subpopulations

Gnomad4 AFR exome

AF:

0.00911

Gnomad4 AMR exome

AF:

0.203

Gnomad4 ASJ exome

AF:

0.0322

Gnomad4 EAS exome

AF:

0.000453

Gnomad4 SAS exome

AF:

0.0208

Gnomad4 FIN exome

AF:

0.114

Gnomad4 NFE exome

AF:

0.0537

Gnomad4 OTH exome

AF:

0.0489

GnomAD4 genome

AF:

0.0528

AC:

8045

AN:

152352

Hom.:

409

Cov.:

AF XY:

0.0559

AC XY:

4166

AN XY:

74500

show subpopulations

Gnomad4 AFR

AF:

0.0112

Gnomad4 AMR

AF:

0.153

Gnomad4 ASJ

AF:

0.0317

Gnomad4 EAS

AF:

0.00193

Gnomad4 SAS

AF:

0.0205

Gnomad4 FIN

AF:

0.110

Gnomad4 NFE

AF:

0.0541

Gnomad4 OTH

AF:

0.0562

Alfa

AF:

0.0437

Hom.:

110

Bravo

AF:

0.0554

TwinsUK

AF:

0.0518

AC:

192

ALSPAC

AF:

0.0547

AC:

211

ESP6500AA

AF:

0.0130

AC:

ESP6500EA

AF:

0.0527

AC:

443

ExAC

AF:

0.0617

AC:

7465

EpiCase

AF:

0.0491

EpiControl

AF:

0.0487

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.17

BayesDel_addAF

Benign

-0.43

BayesDel_noAF

Benign

-0.24

CADD

Benign

DANN

Uncertain

1.0

DEOGEN2

Benign

0.31

Eigen

Uncertain

0.23

Eigen_PC

Benign

0.19

FATHMM_MKL

Pathogenic

0.98

LIST_S2

Uncertain

0.87

MetaRNN

Benign

0.0025

MetaSVM

Benign

-1.1

MutationAssessor

Benign

1.7

MutationTaster

Benign

1.0

D;D;D;D;D

PrimateAI

Uncertain

0.64

PROVEAN

Pathogenic

-7.2

REVEL

Benign

0.24

Sift

Benign

0.033

Sift4G

Pathogenic

0.0

Polyphen

1.0

Vest4

0.93

MPC

0.14

ClinPred

0.036

GERP RS

1.9

Varity_R

0.51

gMVP

0.46

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over