Genetic Variant OR5A2:c.-73A>G (chr11-59423026-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001001954.2(OR5A2):c.-73A>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.271 in 1,442,614 control chromosomes in the GnomAD database, including 54,438 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 0.24 ( 4782 hom., cov: 32)

Exomes 𝑓: 0.27 ( 49656 hom. )

Consequence

OR5A2
NM_001001954.2 5_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.358

Publications

12 publications found

Variant links:

Genes affected

OR5A2 (HGNC:15249): (olfactory receptor family 5 subfamily A 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]

OR5A2 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.88).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.281 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OR5A2	NM_001001954.2 link	c.-73A>G		5_prime_UTR_variant	Exon 2 of 2	ENST00000302040.6	NP_001001954.1	Q8NGI9A0A126GVD5

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
OR5A2	ENST00000302040.6 link	c.-73A>G	5_prime_UTR_variant	Exon 2 of 2	6	NM_001001954.2	ENSP00000303834.4	Q8NGI9
OR5A2	ENST00000641361.1 link	c.-73A>G	5_prime_UTR_variant	Exon 2 of 2			ENSP00000493065.1	Q8NGI9
OR5A2	ENST00000641673.1 link	c.-73A>G	5_prime_UTR_variant	Exon 1 of 1			ENSP00000492975.1	Q8NGI9

Frequencies

GnomAD3 genomes

AF:

0.244

AC:

37092

AN:

151986

Hom.:

4773

Cov.:

show subpopulations

Gnomad AFR

AF:

0.214

Gnomad AMI

AF:

0.171

Gnomad AMR

AF:

0.174

Gnomad ASJ

AF:

0.256

Gnomad EAS

AF:

0.139

Gnomad SAS

AF:

0.164

Gnomad FIN

AF:

0.296

Gnomad MID

AF:

0.285

Gnomad NFE

AF:

0.284

Gnomad OTH

AF:

0.240

GnomAD4 exome

AF:

0.274

AC:

353682

AN:

1290510

Hom.:

49656

Cov.:

AF XY:

0.271

AC XY:

173515

AN XY:

639952

show subpopulations

African (AFR)

AF:

0.216

AC:

6226

AN:

28786

American (AMR)

AF:

0.136

AC:

4493

AN:

33020

Ashkenazi Jewish (ASJ)

AF:

0.272

AC:

5517

AN:

20320

East Asian (EAS)

AF:

0.158

AC:

6103

AN:

38618

South Asian (SAS)

AF:

0.168

AC:

11851

AN:

70446

European-Finnish (FIN)

AF:

0.286

AC:

14010

AN:

49036

Middle Eastern (MID)

AF:

0.263

AC:

1352

AN:

5150

European-Non Finnish (NFE)

AF:

0.293

AC:

290363

AN:

991400

Other (OTH)

AF:

0.256

AC:

13767

AN:

53734

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

13164

26328

39491

52655

65819

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

9546

19092

28638

38184

47730

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.244

AC:

37135

AN:

152104

Hom.:

4782

Cov.:

AF XY:

0.241

AC XY:

17916

AN XY:

74336

show subpopulations

African (AFR)

AF:

0.214

AC:

8883

AN:

41490

American (AMR)

AF:

0.174

AC:

2655

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.256

AC:

889

AN:

3468

East Asian (EAS)

AF:

0.139

AC:

717

AN:

5172

South Asian (SAS)

AF:

0.165

AC:

795

AN:

4824

European-Finnish (FIN)

AF:

0.296

AC:

3131

AN:

10574

Middle Eastern (MID)

AF:

0.279

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.284

AC:

19321

AN:

67982

Other (OTH)

AF:

0.240

AC:

506

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1447

2894

4341

5788

7235

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

382

764

1146

1528

1910

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.266

Hom.:

9021

Bravo

AF:

0.234

Asia WGS

AF:

0.172

AC:

595

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

6.3

(source)

DANN

Benign

0.60

PhyloP100

0.36

Mutation Taster

=100/0

polymorphism

(source)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over