Variant 11-54707244-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_001005272.3(OR4A5):c.360C>T(p.Arg120Arg) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00722 in 1,613,670 control chromosomes in the GnomAD database, including 59 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0057 ( 7 hom., cov: 32)

Exomes 𝑓: 0.0074 ( 52 hom. )

Consequence

OR4A5
NM_001005272.3 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -3.48

Variant links:

Genes affected

OR4A5 (HGNC:15162): (olfactory receptor family 4 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, Jul 2008]

OR4A5 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.65).

BP6

Variant 11-54707244-C-T is Benign according to our data. Variant chr11-54707244-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2641782.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-3.48 with no splicing effect.

BS2

High Homozygotes in GnomAd4 at 7 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OR4A5	NM_001005272.3 linkuse as main transcript	c.360C>T	p.Arg120Arg	synonymous_variant	1/1	ENST00000319760.8	NP_001005272.3	Q8NH83A0A126GWJ2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OR4A5	ENST00000319760.8 linkuse as main transcript	c.360C>T	p.Arg120Arg	synonymous_variant	1/1	6	NM_001005272.3	ENSP00000367664.2		Q8NH83

Frequencies

GnomAD3 genomes

AF:

0.00575

AC:

875

AN:

152124

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00176

Gnomad AMI

AF:

0.0439

Gnomad AMR

AF:

0.00302

Gnomad ASJ

AF:

0.00144

Gnomad EAS

AF:

0.00116

Gnomad SAS

AF:

0.00393

Gnomad FIN

AF:

0.0117

Gnomad MID

AF:

0.0158

Gnomad NFE

AF:

0.00804

Gnomad OTH

AF:

0.00478

GnomAD3 exomes

AF:

0.00582

AC:

1458

AN:

250724

Hom.:

AF XY:

0.00578

AC XY:

783

AN XY:

135520

show subpopulations

Gnomad AFR exome

AF:

0.00129

Gnomad AMR exome

AF:

0.00342

Gnomad ASJ exome

AF:

0.00298

Gnomad EAS exome

AF:

0.000822

Gnomad SAS exome

AF:

0.00258

Gnomad FIN exome

AF:

0.0111

Gnomad NFE exome

AF:

0.00806

Gnomad OTH exome

AF:

0.00671

GnomAD4 exome

AF:

0.00738

AC:

10779

AN:

1461428

Hom.:

Cov.:

AF XY:

0.00719

AC XY:

5229

AN XY:

727032

show subpopulations

Gnomad4 AFR exome

AF:

0.00120

Gnomad4 AMR exome

AF:

0.00336

Gnomad4 ASJ exome

AF:

0.00329

Gnomad4 EAS exome

AF:

0.000278

Gnomad4 SAS exome

AF:

0.00290

Gnomad4 FIN exome

AF:

0.0102

Gnomad4 NFE exome

AF:

0.00836

Gnomad4 OTH exome

AF:

0.00565

GnomAD4 genome

AF:

0.00575

AC:

875

AN:

152242

Hom.:

Cov.:

AF XY:

0.00536

AC XY:

399

AN XY:

74438

show subpopulations

Gnomad4 AFR

AF:

0.00176

Gnomad4 AMR

AF:

0.00301

Gnomad4 ASJ

AF:

0.00144

Gnomad4 EAS

AF:

0.00116

Gnomad4 SAS

AF:

0.00394

Gnomad4 FIN

AF:

0.0117

Gnomad4 NFE

AF:

0.00804

Gnomad4 OTH

AF:

0.00473

Alfa

AF:

0.00706

Hom.:

Bravo

AF:

0.00538

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

Nov 01, 2022

OR4A5: BP4, BP7, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.65

CADD

Benign

DANN

Benign

0.49

Splicing

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