chr9-122487205-G-A

Position:

• chr9-122487205-G-A

Variant summary

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

The XM_024447516.2(OR1J2):​c.-189-15490G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.637 in 152,034 control chromosomes in the GnomAD database, including 32,555 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 0.64 (32555 hom., cov: 31)
• Consequence: OR1J2 XM_024447516.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.163

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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.857 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OR1J2	XM_024447516.2	c.-189-15490G>A		intron_variant			XP_024303284.1
OR1J2	XM_024447517.2	c.-107+11390G>A		intron_variant			XP_024303285.1
OR1J2	XR_007061271.1	n.1364+11390G>A		intron_variant
OR1J2	XR_007061274.1	n.1598-393G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000234156	ENST00000431442.2	n.1187-15490G>A		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.637 AC: 96732 AN: 151918 Hom.: 32492 Cov.: 31

Gnomad AFR AF: 0.864

Gnomad AMI AF: 0.575

Gnomad AMR AF: 0.612

Gnomad ASJ AF: 0.497

Gnomad EAS AF: 0.519

Gnomad SAS AF: 0.647

Gnomad FIN AF: 0.598

Gnomad MID AF: 0.583

Gnomad NFE AF: 0.527

Gnomad OTH AF: 0.589

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

GnomAD4 genome AF: 0.637 AC: 96861 AN: 152034 Hom.: 32555 Cov.: 31 AF XY: 0.639 AC XY: 47487 AN XY: 74304

Gnomad4 AFR AF: 0.865

Gnomad4 AMR AF: 0.612

Gnomad4 ASJ AF: 0.497

Gnomad4 EAS AF: 0.519

Gnomad4 SAS AF: 0.647

Gnomad4 FIN AF: 0.598

Gnomad4 NFE AF: 0.527

Gnomad4 OTH AF: 0.593

Alfa AF: 0.583 Hom.: 11058

Bravo AF: 0.645

Asia WGS AF: 0.637 AC: 2215 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.51
DANN	Benign	0.16

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4837971; hg19: chr9-125249484;