rs7120612

Variant names:

• chr11-5132927-A-G
• rs7120612
• NM_001005160.3:c.-60-225T>C

Variant summary

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

The NM_001005160.3(OR52A5):​c.-60-225T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.21 in 152,106 control chromosomes in the GnomAD database, including 3,712 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 0.21 (3712 hom., cov: 32)
• Consequence: OR52A5 NM_001005160.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0860

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=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.309 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OR52A5	NM_001005160.3	c.-60-225T>C		intron_variant	Intron 1 of 1	ENST00000307388.2	NP_001005160.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OR52A5	ENST00000307388.2	c.-60-225T>C		intron_variant	Intron 1 of 1	6	NM_001005160.3	ENSP00000303469.1
OR52A5	ENST00000642125.1	c.-60-225T>C		intron_variant	Intron 1 of 1			ENSP00000493298.1

Frequencies

GnomAD3 genomes AF: 0.210 AC: 31861 AN: 151988 Hom.: 3709 Cov.: 32

Gnomad AFR AF: 0.139

Gnomad AMI AF: 0.116

Gnomad AMR AF: 0.247

Gnomad ASJ AF: 0.315

Gnomad EAS AF: 0.0256

Gnomad SAS AF: 0.321

Gnomad FIN AF: 0.203

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.246

Gnomad OTH AF: 0.244

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.210 AC: 31885 AN: 152106 Hom.: 3712 Cov.: 32 AF XY: 0.210 AC XY: 15630 AN XY: 74350

Gnomad4 AFR AF: 0.139

Gnomad4 AMR AF: 0.247

Gnomad4 ASJ AF: 0.315

Gnomad4 EAS AF: 0.0257

Gnomad4 SAS AF: 0.322

Gnomad4 FIN AF: 0.203

Gnomad4 NFE AF: 0.246

Gnomad4 OTH AF: 0.243

Alfa AF: 0.243 Hom.: 2316

Bravo AF: 0.208

Asia WGS AF: 0.173 AC: 601 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	3.1
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7120612; hg19: chr11-5154157;