rs11602535

Variant names:

• chr11-59423026-T-C
• rs11602535
• NM_001001954.2:c.-73A>G

Variant summary

Our verdict is Benign. The variant received -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
• 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]

ACMG classification

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001001954.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OR5A2	NM_001001954.2	MANE Select	c.-73A>G		5_prime_UTR	Exon 2 of 2	NP_001001954.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OR5A2	ENST00000302040.6	TSL:6 MANE Select	c.-73A>G		5_prime_UTR	Exon 2 of 2	ENSP00000303834.4
	OR5A2	ENST00000641361.1		c.-73A>G		5_prime_UTR	Exon 2 of 2	ENSP00000493065.1
	OR5A2	ENST00000641673.1		c.-73A>G		5_prime_UTR	Exon 1 of 1	ENSP00000492975.1

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

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

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

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: 82 AN: 294

European-Non Finnish (NFE) AF: 0.284 AC: 19321 AN: 67982

Other (OTH) AF: 0.240 AC: 506 AN: 2108

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.3
DANN	Benign	0.60
PhyloP100		0.36
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs11602535; hg19: chr11-59190499;