rs9332460

Variant names:

• chr9-122473276-A-G
• rs9332460
• ENST00000412262.2:n.57-1802A>G

Your query was ambiguous. Multiple possible variants found:

• chr9-122473276-A-G
• chr9-122473276-A-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000412262.2(ENSG00000234156):​n.57-1802A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.259 in 152,084 control chromosomes in the GnomAD database, including 5,814 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 0.26 (5814 hom., cov: 32)
• Consequence: ENSG00000234156 ENST00000412262.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.77
• Publications: 2 publications found

Genes affected

ENSG00000234156 (HGNC:):

OR1J2 (HGNC:8209): (olfactory receptor family 1 subfamily J 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=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.39 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OR1J2	XM_024447516.2	c.-190+4091A>G		intron_variant	Intron 1 of 2		XP_024303284.1
OR1J2	XM_024447517.2	c.-230-2416A>G		intron_variant	Intron 1 of 3		XP_024303285.1
OR1J2	XR_007061271.1	n.1241-2416A>G		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000234156	ENST00000412262.2	n.57-1802A>G		intron_variant	Intron 1 of 2	3
ENSG00000234156	ENST00000431442.3	n.1186+4091A>G		intron_variant	Intron 6 of 9	3
ENSG00000234156	ENST00000650686.1	n.850-2416A>G		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.259 AC: 39391 AN: 151966 Hom.: 5789 Cov.: 32

Gnomad AFR AF: 0.394

Gnomad AMI AF: 0.133

Gnomad AMR AF: 0.176

Gnomad ASJ AF: 0.162

Gnomad EAS AF: 0.384

Gnomad SAS AF: 0.199

Gnomad FIN AF: 0.298

Gnomad MID AF: 0.172

Gnomad NFE AF: 0.193

Gnomad OTH AF: 0.214

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

GnomAD4 genome AF: 0.259 AC: 39464 AN: 152084 Hom.: 5814 Cov.: 32 AF XY: 0.261 AC XY: 19408 AN XY: 74348

African (AFR) AF: 0.395 AC: 16395 AN: 41480

American (AMR) AF: 0.176 AC: 2689 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.162 AC: 563 AN: 3468

East Asian (EAS) AF: 0.384 AC: 1980 AN: 5160

South Asian (SAS) AF: 0.198 AC: 953 AN: 4812

European-Finnish (FIN) AF: 0.298 AC: 3149 AN: 10584

Middle Eastern (MID) AF: 0.175 AC: 51 AN: 292

European-Non Finnish (NFE) AF: 0.193 AC: 13109 AN: 67960

Other (OTH) AF: 0.215 AC: 454 AN: 2112

Alfa AF: 0.234 Hom.: 1689

Bravo AF: 0.254

Asia WGS AF: 0.283 AC: 986 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.52
DANN	Benign	0.48
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs9332460; hg19: chr9-125235555;