9-122473276-A-G

Position:

• chr9-122473276-A-G

Variant summary

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

The XM_024447516.2(OR1J2):​c.-190+4091A>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: OR1J2 XM_024447516.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.77

Genes affected

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]

ENSG00000234156 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
OR1J2	XM_024447516.2	c.-190+4091A>G		intron_variant			XP_024303284.1
OR1J2	XM_024447517.2	c.-230-2416A>G		intron_variant			XP_024303285.1
OR1J2	XR_007061271.1	n.1241-2416A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000234156	ENST00000412262.2	n.57-1802A>G		intron_variant		3
ENSG00000234156	ENST00000431442.2	n.1186+4091A>G		intron_variant		3
ENSG00000234156	ENST00000650686.1	n.850-2416A>G		intron_variant

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

Gnomad4 AFR AF: 0.395

Gnomad4 AMR AF: 0.176

Gnomad4 ASJ AF: 0.162

Gnomad4 EAS AF: 0.384

Gnomad4 SAS AF: 0.198

Gnomad4 FIN AF: 0.298

Gnomad4 NFE AF: 0.193

Gnomad4 OTH AF: 0.215

Alfa AF: 0.225 Hom.: 868

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9332460; hg19: chr9-125235555;