9-122468813-A-G

Variant names:

• chr9-122468813-A-G
• rs2778636
• ENST00000431442.2:n.814A>G

Variant summary

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

The ENST00000431442.2(ENSG00000234156):​n.814A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.632 in 152,050 control chromosomes in the GnomAD database, including 30,794 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 0.63 (30794 hom., cov: 32)
• Consequence: ENSG00000234156 ENST00000431442.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.689 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OR1J2	XR_007061271.1	n.868A>G		non_coding_transcript_exon_variant	Exon 2 of 5
OR1J2	XR_007061272.1	n.487A>G		non_coding_transcript_exon_variant	Exon 3 of 5
OR1J2	XR_007061273.1	n.487A>G		non_coding_transcript_exon_variant	Exon 3 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000234156	ENST00000431442.2	n.814A>G		non_coding_transcript_exon_variant	Exon 6 of 10	3
ENSG00000234156	ENST00000433572.3	n.848A>G		non_coding_transcript_exon_variant	Exon 7 of 7	3
ENSG00000234156	ENST00000650686.1	n.477A>G		non_coding_transcript_exon_variant	Exon 3 of 4

Frequencies

GnomAD3 genomes AF: 0.633 AC: 96107 AN: 151932 Hom.: 30780 Cov.: 32

Gnomad AFR AF: 0.555

Gnomad AMI AF: 0.664

Gnomad AMR AF: 0.630

Gnomad ASJ AF: 0.747

Gnomad EAS AF: 0.478

Gnomad SAS AF: 0.679

Gnomad FIN AF: 0.544

Gnomad MID AF: 0.728

Gnomad NFE AF: 0.695

Gnomad OTH AF: 0.677

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

GnomAD4 genome AF: 0.632 AC: 96153 AN: 152050 Hom.: 30794 Cov.: 32 AF XY: 0.628 AC XY: 46649 AN XY: 74308

Gnomad4 AFR AF: 0.554

Gnomad4 AMR AF: 0.630

Gnomad4 ASJ AF: 0.747

Gnomad4 EAS AF: 0.479

Gnomad4 SAS AF: 0.680

Gnomad4 FIN AF: 0.544

Gnomad4 NFE AF: 0.694

Gnomad4 OTH AF: 0.675

Alfa AF: 0.693 Hom.: 30194

Bravo AF: 0.635

Asia WGS AF: 0.574 AC: 1997 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.3
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2778636; hg19: chr9-125231092;