Variant chr11-5967683-A-G 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_001146033.1(OR56A5):c.812T>C(p.Ile271Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00625 in 1,613,878 control chromosomes in the GnomAD database, including 51 homozygotes. In-silico tool predicts a benign outcome for this variant. 8/13 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0055 ( 7 hom., cov: 33)

Exomes 𝑓: 0.0063 ( 44 hom. )

Consequence

OR56A5
NM_001146033.1 missense

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 2.97

Variant links:

Genes affected

OR56A5 (HGNC:14792): (olfactory receptor family 56 subfamily A member 5) 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, Mar 2009]

OR56A5 links:

OR56A3 (HGNC:):

OR56A3 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.006551355).

BP6

Variant 11-5967683-A-G is Benign according to our data. Variant chr11-5967683-A-G is described in ClinVar as [Benign]. Clinvar id is 2641545.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAd4 at 7 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
OR56A5	NM_001146033.1 linkuse as main transcript	c.812T>C	p.Ile271Thr	missense_variant	1/1	ENST00000532411.2
OR56A3	XM_047426926.1 linkuse as main transcript	c.*468+18921A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
OR56A5	ENST00000532411.2 linkuse as main transcript	c.812T>C	p.Ile271Thr	missense_variant	1/1		NM_001146033.1	P1

Frequencies

GnomAD3 genomes

AF:

0.00548

AC:

834

AN:

152216

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00106

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00222

Gnomad ASJ

AF:

0.000288

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00207

Gnomad FIN

AF:

0.0318

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.00591

Gnomad OTH

AF:

0.00191

GnomAD3 exomes

AF:

0.00649

AC:

1626

AN:

250678

Hom.:

AF XY:

0.00666

AC XY:

902

AN XY:

135430

show subpopulations

Gnomad AFR exome

AF:

0.000865

Gnomad AMR exome

AF:

0.00183

Gnomad ASJ exome

AF:

0.000298

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00197

Gnomad FIN exome

AF:

0.0283

Gnomad NFE exome

AF:

0.00736

Gnomad OTH exome

AF:

0.00621

GnomAD4 exome

AF:

0.00633

AC:

9248

AN:

1461544

Hom.:

Cov.:

AF XY:

0.00624

AC XY:

4535

AN XY:

726996

show subpopulations

Gnomad4 AFR exome

AF:

0.000747

Gnomad4 AMR exome

AF:

0.00202

Gnomad4 ASJ exome

AF:

0.000268

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00203

Gnomad4 FIN exome

AF:

0.0281

Gnomad4 NFE exome

AF:

0.00640

Gnomad4 OTH exome

AF:

0.00543

GnomAD4 genome

AF:

0.00547

AC:

833

AN:

152334

Hom.:

Cov.:

AF XY:

0.00634

AC XY:

472

AN XY:

74488

show subpopulations

Gnomad4 AFR

AF:

0.00106

Gnomad4 AMR

AF:

0.00222

Gnomad4 ASJ

AF:

0.000288

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00187

Gnomad4 FIN

AF:

0.0318

Gnomad4 NFE

AF:

0.00591

Gnomad4 OTH

AF:

0.00189

Alfa

AF:

0.00510

Hom.:

Bravo

AF:

0.00308

TwinsUK

AF:

0.00620

AC:

ALSPAC

AF:

0.00571

AC:

ESP6500AA

AF:

0.000723

AC:

ESP6500EA

AF:

0.00471

AC:

ExAC

AF:

0.00672

AC:

816

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Jul 01, 2022

OR56A5: BP4, BS1, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Pathogenic

0.57

BayesDel_addAF

Benign

-0.25

BayesDel_noAF

Benign

-0.13

CADD

Benign

DANN

Benign

0.66

DEOGEN2

Benign

0.016

.;T

FATHMM_MKL

Benign

0.27

LIST_S2

Benign

0.73

T;T

MetaRNN

Benign

0.0066

T;T

MutationAssessor

Uncertain

2.2

.;M

PrimateAI

Benign

0.29

Sift4G

Uncertain

0.0030

D;D

Polyphen

0.96

.;D

Vest4

0.087

MVP

0.22

GERP RS

3.7

Varity_R

0.073

gMVP

0.10

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over