chr11-59423026-T-C
Variant names:
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
NM_001001954.2 5_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.358
Publications
12 publications found
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]
Genome browser will be placed here
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 | c.-73A>G | 5_prime_UTR_variant | Exon 2 of 2 | ENST00000302040.6 | NP_001001954.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
OR5A2 | ENST00000302040.6 | c.-73A>G | 5_prime_UTR_variant | Exon 2 of 2 | 6 | NM_001001954.2 | ENSP00000303834.4 | |||
OR5A2 | ENST00000641361.1 | c.-73A>G | 5_prime_UTR_variant | Exon 2 of 2 | ENSP00000493065.1 | |||||
OR5A2 | ENST00000641673.1 | c.-73A>G | 5_prime_UTR_variant | Exon 1 of 1 | ENSP00000492975.1 |
Frequencies
GnomAD3 genomes AF: 0.244 AC: 37092AN: 151986Hom.: 4773 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
37092
AN:
151986
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.274 AC: 353682AN: 1290510Hom.: 49656 Cov.: 19 AF XY: 0.271 AC XY: 173515AN XY: 639952 show subpopulations
GnomAD4 exome
AF:
AC:
353682
AN:
1290510
Hom.:
Cov.:
19
AF XY:
AC XY:
173515
AN XY:
639952
show subpopulations
African (AFR)
AF:
AC:
6226
AN:
28786
American (AMR)
AF:
AC:
4493
AN:
33020
Ashkenazi Jewish (ASJ)
AF:
AC:
5517
AN:
20320
East Asian (EAS)
AF:
AC:
6103
AN:
38618
South Asian (SAS)
AF:
AC:
11851
AN:
70446
European-Finnish (FIN)
AF:
AC:
14010
AN:
49036
Middle Eastern (MID)
AF:
AC:
1352
AN:
5150
European-Non Finnish (NFE)
AF:
AC:
290363
AN:
991400
Other (OTH)
AF:
AC:
13767
AN:
53734
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.507
Heterozygous variant carriers
0
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
0
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: 37135AN: 152104Hom.: 4782 Cov.: 32 AF XY: 0.241 AC XY: 17916AN XY: 74336 show subpopulations
GnomAD4 genome
AF:
AC:
37135
AN:
152104
Hom.:
Cov.:
32
AF XY:
AC XY:
17916
AN XY:
74336
show subpopulations
African (AFR)
AF:
AC:
8883
AN:
41490
American (AMR)
AF:
AC:
2655
AN:
15282
Ashkenazi Jewish (ASJ)
AF:
AC:
889
AN:
3468
East Asian (EAS)
AF:
AC:
717
AN:
5172
South Asian (SAS)
AF:
AC:
795
AN:
4824
European-Finnish (FIN)
AF:
AC:
3131
AN:
10574
Middle Eastern (MID)
AF:
AC:
82
AN:
294
European-Non Finnish (NFE)
AF:
AC:
19321
AN:
67982
Other (OTH)
AF:
AC:
506
AN:
2108
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
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
0
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:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
595
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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