rs11602535

chr11-59423026-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.358

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]

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
OR5A2	NM_001001954.2	c.-73A>G		5_prime_UTR_variant	2/2	ENST00000302040.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
OR5A2	ENST00000302040.6	c.-73A>G		5_prime_UTR_variant	2/2		NM_001001954.2	P1
OR5A2	ENST00000641361.1	c.-73A>G		5_prime_UTR_variant	2/2			P1
OR5A2	ENST00000641673.1	c.-73A>G		5_prime_UTR_variant	1/1			P1

Frequencies

GnomAD3 genomes AF: 0.244 AC: 37092 AN: 151986 Hom.: 4773 Cov.: 32

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.: 19 AF XY: 0.271 AC XY: 173515 AN XY: 639952

Gnomad4 AFR exome AF: 0.216

Gnomad4 AMR exome AF: 0.136

Gnomad4 ASJ exome AF: 0.272

Gnomad4 EAS exome AF: 0.158

Gnomad4 SAS exome AF: 0.168

Gnomad4 FIN exome AF: 0.286

Gnomad4 NFE exome AF: 0.293

Gnomad4 OTH exome AF: 0.256

GnomAD4 genome AF: 0.244 AC: 37135 AN: 152104 Hom.: 4782 Cov.: 32 AF XY: 0.241 AC XY: 17916 AN XY: 74336

Gnomad4 AFR AF: 0.214

Gnomad4 AMR AF: 0.174

Gnomad4 ASJ AF: 0.256

Gnomad4 EAS AF: 0.139

Gnomad4 SAS AF: 0.165

Gnomad4 FIN AF: 0.296

Gnomad4 NFE AF: 0.284

Gnomad4 OTH AF: 0.240

Alfa AF: 0.270 Hom.: 7333

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
Dann	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11602535; hg19: chr11-59190499;