rs2499949

Positions:

• chr11-5130286-G-A
• chr11-5130286-G-T

Variant summary

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

The NM_001005160.3(OR52A5):​c.*1406C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.172 in 151,670 control chromosomes in the GnomAD database, including 2,837 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 0.17 (2837 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: OR52A5 NM_001005160.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.116

Genes affected

OR52A5 (HGNC:19580): (olfactory receptor family 52 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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.357 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OR52A5	NM_001005160.3	c.*1406C>T		3_prime_UTR_variant	2/2	ENST00000307388.2	NP_001005160.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OR52A5	ENST00000307388.2	c.*1406C>T		3_prime_UTR_variant	2/2		NM_001005160.3	ENSP00000303469	P1
OR52A5	ENST00000642125.1	c.*1406C>T		3_prime_UTR_variant	2/2			ENSP00000493298	P1

Frequencies

GnomAD3 genomes AF: 0.172 AC: 26134 AN: 151546 Hom.: 2833 Cov.: 32

Gnomad AFR AF: 0.0471

Gnomad AMI AF: 0.0844

Gnomad AMR AF: 0.208

Gnomad ASJ AF: 0.153

Gnomad EAS AF: 0.372

Gnomad SAS AF: 0.233

Gnomad FIN AF: 0.212

Gnomad MID AF: 0.107

Gnomad NFE AF: 0.218

Gnomad OTH AF: 0.168

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.172 AC: 26143 AN: 151670 Hom.: 2837 Cov.: 32 AF XY: 0.176 AC XY: 13003 AN XY: 74082

Gnomad4 AFR AF: 0.0469

Gnomad4 AMR AF: 0.208

Gnomad4 ASJ AF: 0.153

Gnomad4 EAS AF: 0.371

Gnomad4 SAS AF: 0.233

Gnomad4 FIN AF: 0.212

Gnomad4 NFE AF: 0.218

Gnomad4 OTH AF: 0.172

Alfa AF: 0.207 Hom.: 1794

Bravo AF: 0.166

Asia WGS AF: 0.315 AC: 1082 AN: 3434

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.4
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2499949; hg19: chr11-5151516;