NM_001348233.2:c.-367T>C

Variant names:

• chr14-22644437-A-G
• rs9323178
• NM_001348233.2:c.-367T>C

Variant summary

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

The NM_001348233.2(OR6J1):​c.-367T>C variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.581 in 152,048 control chromosomes in the GnomAD database, including 27,431 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 0.58 (27429 hom., cov: 31)
  • Exomes 𝑓: 0.50 (2 hom.)
• Consequence: OR6J1 NM_001348233.2 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.413
• Publications: 8 publications found

Genes affected

OR6J1 (HGNC:14707): (olfactory receptor family 6 subfamily J member 1) 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. This olfactory receptor gene is a segregating pseudogene, where some individuals have an allele that encodes a functional olfactory receptor, while other individuals have an allele encoding a protein that is predicted to be non-functional. [provided by RefSeq, Jan 2017]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.802 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001348233.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OR6J1	NM_001348233.2	MANE Select	c.-367T>C		upstream_gene	N/A	NP_001335162.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OR6J1	ENST00000540461.2	TSL:6 MANE Select	c.-367T>C		upstream_gene	N/A	ENSP00000437629.1

Frequencies

GnomAD3 genomes AF: 0.581 AC: 88234 AN: 151914 Hom.: 27393 Cov.: 31

Gnomad AFR AF: 0.809

Gnomad AMI AF: 0.622

Gnomad AMR AF: 0.418

Gnomad ASJ AF: 0.455

Gnomad EAS AF: 0.274

Gnomad SAS AF: 0.488

Gnomad FIN AF: 0.498

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.529

Gnomad OTH AF: 0.532

GnomAD4 exome AF: 0.500 AC: 7 AN: 14 Hom.: 2 AF XY: 0.625 AC XY: 5 AN XY: 8

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.500 AC: 7 AN: 14

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.581 AC: 88309 AN: 152034 Hom.: 27429 Cov.: 31 AF XY: 0.573 AC XY: 42553 AN XY: 74304

African (AFR) AF: 0.809 AC: 33556 AN: 41480

American (AMR) AF: 0.417 AC: 6368 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.455 AC: 1576 AN: 3466

East Asian (EAS) AF: 0.274 AC: 1415 AN: 5168

South Asian (SAS) AF: 0.487 AC: 2348 AN: 4826

European-Finnish (FIN) AF: 0.498 AC: 5263 AN: 10564

Middle Eastern (MID) AF: 0.514 AC: 151 AN: 294

European-Non Finnish (NFE) AF: 0.529 AC: 35958 AN: 67944

Other (OTH) AF: 0.525 AC: 1107 AN: 2108

Alfa AF: 0.537 Hom.: 38712

Bravo AF: 0.581

Asia WGS AF: 0.363 AC: 1266 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.5
DANN	Benign	0.44
PhyloP100		-0.41
PromoterAI		-0.023	Neutral

Splicing

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

Other links and lift over

dbSNP: rs9323178; hg19: chr14-23113646;