Variant 11-56641733-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The NM_001002925.1(OR5AP2):c.707C>T(p.Ser236Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00344 in 1,614,006 control chromosomes in the GnomAD database, including 25 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0030 ( 3 hom., cov: 32)

Exomes 𝑓: 0.0035 ( 22 hom. )

Consequence

OR5AP2
NM_001002925.1 missense

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.57

Variant links:

Genes affected

OR5AP2 (HGNC:15258): (olfactory receptor family 5 subfamily AP member 2) Olfactory receptors interact with odorant molecules in the nose, to initiate a neuronal response that triggers the perception of a smell. The olfactory receptor proteins are members of a large family of G-protein-coupled receptors (GPCR) arising from single coding-exon genes. Olfactory receptors share a 7-transmembrane domain structure with many neurotransmitter and hormone receptors and are responsible for the recognition and G protein-mediated transduction of odorant signals. The olfactory receptor gene family is the largest in the genome. The nomenclature assigned to the olfactory receptor genes and proteins for this organism is independent of other organisms. [provided by RefSeq, Jul 2008]

OR5AP2 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.005096644).

BP6

Variant 11-56641733-G-A is Benign according to our data. Variant chr11-56641733-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2641789.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAd4 at 3 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OR5AP2	NM_001002925.1 linkuse as main transcript	c.707C>T	p.Ser236Leu	missense_variant	1/1	ENST00000544374.3	NP_001002925.1	Q8NGF4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OR5AP2	ENST00000544374.3 linkuse as main transcript	c.707C>T	p.Ser236Leu	missense_variant	1/1	6	NM_001002925.1	ENSP00000442701.2		Q8NGF4

Frequencies

GnomAD3 genomes

AF:

0.00304

AC:

462

AN:

152158

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000869

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00353

Gnomad ASJ

AF:

0.0343

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000829

Gnomad FIN

AF:

0.0000943

Gnomad MID

AF:

0.0222

Gnomad NFE

AF:

0.00335

Gnomad OTH

AF:

0.00621

GnomAD3 exomes

AF:

0.00316

AC:

795

AN:

251408

Hom.:

AF XY:

0.00302

AC XY:

410

AN XY:

135878

show subpopulations

Gnomad AFR exome

AF:

0.000800

Gnomad AMR exome

AF:

0.00234

Gnomad ASJ exome

AF:

0.0262

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00121

Gnomad FIN exome

AF:

0.000139

Gnomad NFE exome

AF:

0.00320

Gnomad OTH exome

AF:

0.00538

GnomAD4 exome

AF:

0.00348

AC:

5087

AN:

1461730

Hom.:

Cov.:

AF XY:

0.00341

AC XY:

2483

AN XY:

727176

show subpopulations

Gnomad4 AFR exome

AF:

0.000866

Gnomad4 AMR exome

AF:

0.00264

Gnomad4 ASJ exome

AF:

0.0292

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00155

Gnomad4 FIN exome

AF:

0.000131

Gnomad4 NFE exome

AF:

0.00327

Gnomad4 OTH exome

AF:

0.00568

GnomAD4 genome

AF:

0.00303

AC:

462

AN:

152276

Hom.:

Cov.:

AF XY:

0.00273

AC XY:

203

AN XY:

74448

show subpopulations

Gnomad4 AFR

AF:

0.000866

Gnomad4 AMR

AF:

0.00353

Gnomad4 ASJ

AF:

0.0343

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000829

Gnomad4 FIN

AF:

0.0000943

Gnomad4 NFE

AF:

0.00335

Gnomad4 OTH

AF:

0.00615

Alfa

AF:

0.00433

Hom.:

Bravo

AF:

0.00323

TwinsUK

AF:

0.00431

AC:

ALSPAC

AF:

0.00182

AC:

ESP6500AA

AF:

0.00114

AC:

ESP6500EA

AF:

0.00407

AC:

ExAC

AF:

0.00270

AC:

328

Asia WGS

AF:

0.000577

AC:

AN:

3478

EpiCase

AF:

0.00354

EpiControl

AF:

0.00314

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Jan 01, 2023

OR5AP2: BP4, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.11

BayesDel_addAF

Benign

-0.41

BayesDel_noAF

Benign

-0.36

CADD

Uncertain

DANN

Uncertain

1.0

DEOGEN2

Benign

0.011

Eigen

Uncertain

0.30

Eigen_PC

Benign

0.065

FATHMM_MKL

Benign

0.12

LIST_S2

Uncertain

0.91

M_CAP

Benign

0.0031

MetaRNN

Benign

0.0051

MetaSVM

Benign

-1.0

MutationAssessor

Pathogenic

3.3

PrimateAI

Benign

0.26

REVEL

Benign

0.096

Polyphen

1.0

MVP

0.51

ClinPred

0.046

GERP RS

4.2

Varity_R

0.66

gMVP

0.11

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over