Variant 11-77103064-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_006189.1(OMP):c.225G>A(p.Pro75=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.21 in 1,613,472 control chromosomes in the GnomAD database, including 36,614 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 0.21 ( 3416 hom., cov: 33)

Exomes 𝑓: 0.21 ( 33198 hom. )

Consequence

OMP
NM_006189.1 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -6.47

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 -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.84).

BP7

Synonymous conserved (PhyloP=-6.47 with no splicing effect.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.306 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein
OMP	NM_006189.1 linkuse as main transcript	c.225G>A	p.Pro75=	synonymous_variant	1/1	ENST00000529803.1	NP_006180.1
CAPN5	NM_004055.5 linkuse as main transcript	c.297+9251G>A		intron_variant		ENST00000648180.1	NP_004046.2
CAPN5	XM_011545225.1 linkuse as main transcript	c.417+9251G>A		intron_variant			XP_011543527.1
CAPN5	XM_017018223.3 linkuse as main transcript	c.405+9251G>A		intron_variant			XP_016873712.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OMP	ENST00000529803.1 linkuse as main transcript	c.225G>A	p.Pro75=	synonymous_variant	1/1		NM_006189.1	ENSP00000436376	P1
CAPN5	ENST00000648180.1 linkuse as main transcript	c.297+9251G>A		intron_variant			NM_004055.5	ENSP00000498132	P1

Frequencies

GnomAD3 genomes

AF:

0.207

AC:

31523

AN:

152058

Hom.:

3409

Cov.:

show subpopulations

Gnomad AFR

AF:

0.194

Gnomad AMI

AF:

0.135

Gnomad AMR

AF:

0.213

Gnomad ASJ

AF:

0.176

Gnomad EAS

AF:

0.228

Gnomad SAS

AF:

0.318

Gnomad FIN

AF:

0.246

Gnomad MID

AF:

0.201

Gnomad NFE

AF:

0.201

Gnomad OTH

AF:

0.210

GnomAD3 exomes

AF:

0.218

AC:

54044

AN:

248082

Hom.:

6139

AF XY:

0.222

AC XY:

29983

AN XY:

134788

show subpopulations

Gnomad AFR exome

AF:

0.196

Gnomad AMR exome

AF:

0.193

Gnomad ASJ exome

AF:

0.179

Gnomad EAS exome

AF:

0.232

Gnomad SAS exome

AF:

0.308

Gnomad FIN exome

AF:

0.242

Gnomad NFE exome

AF:

0.201

Gnomad OTH exome

AF:

0.210

GnomAD4 exome

AF:

0.211

AC:

307650

AN:

1461294

Hom.:

33198

Cov.:

AF XY:

0.213

AC XY:

154799

AN XY:

726926

show subpopulations

Gnomad4 AFR exome

AF:

0.199

Gnomad4 AMR exome

AF:

0.196

Gnomad4 ASJ exome

AF:

0.185

Gnomad4 EAS exome

AF:

0.224

Gnomad4 SAS exome

AF:

0.303

Gnomad4 FIN exome

AF:

0.236

Gnomad4 NFE exome

AF:

0.203

Gnomad4 OTH exome

AF:

0.217

GnomAD4 genome

AF:

0.207

AC:

31556

AN:

152178

Hom.:

3416

Cov.:

AF XY:

0.211

AC XY:

15673

AN XY:

74380

show subpopulations

Gnomad4 AFR

AF:

0.194

Gnomad4 AMR

AF:

0.213

Gnomad4 ASJ

AF:

0.176

Gnomad4 EAS

AF:

0.229

Gnomad4 SAS

AF:

0.319

Gnomad4 FIN

AF:

0.246

Gnomad4 NFE

AF:

0.201

Gnomad4 OTH

AF:

0.212

Alfa

AF:

0.202

Hom.:

6514

Bravo

AF:

0.200

Asia WGS

AF:

0.281

AC:

977

AN:

3478

EpiCase

AF:

0.196

EpiControl

AF:

0.196

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

5.2

DANN

Benign

0.87

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.070

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