rs857819

Variant names:

• chr1-158764770-C-T
• rs857819
• NM_001005185.2:c.*974G>A

Variant summary

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

The NM_001005185.2(OR6N1):​c.*974G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.437 in 151,770 control chromosomes in the GnomAD database, including 15,140 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 0.44 (15140 hom., cov: 31)
  • Failed GnomAD Quality Control
• Consequence: OR6N1 NM_001005185.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09
• Publications: 7 publications found

Genes affected

OR6N1 (HGNC:15034): (olfactory receptor family 6 subfamily N 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. [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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.587 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001005185.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OR6N1	NM_001005185.2	MANE Select	c.*974G>A		3_prime_UTR	Exon 2 of 2	NP_001005185.1	Q8NGY5

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OR6N1	ENST00000641846.1	MANE Select	c.*974G>A		3_prime_UTR	Exon 2 of 2	ENSP00000493254.1	Q8NGY5
	OR6N1	ENST00000641189.1		n.175+7251G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.437 AC: 66330 AN: 151652 Hom.: 15120 Cov.: 31

Gnomad AFR AF: 0.321

Gnomad AMI AF: 0.507

Gnomad AMR AF: 0.564

Gnomad ASJ AF: 0.439

Gnomad EAS AF: 0.605

Gnomad SAS AF: 0.271

Gnomad FIN AF: 0.475

Gnomad MID AF: 0.357

Gnomad NFE AF: 0.472

Gnomad OTH AF: 0.456

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

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) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.437 AC: 66376 AN: 151770 Hom.: 15140 Cov.: 31 AF XY: 0.437 AC XY: 32424 AN XY: 74156

African (AFR) AF: 0.321 AC: 13297 AN: 41394

American (AMR) AF: 0.564 AC: 8622 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.439 AC: 1522 AN: 3466

East Asian (EAS) AF: 0.605 AC: 3129 AN: 5172

South Asian (SAS) AF: 0.269 AC: 1294 AN: 4804

European-Finnish (FIN) AF: 0.475 AC: 4974 AN: 10482

Middle Eastern (MID) AF: 0.360 AC: 105 AN: 292

European-Non Finnish (NFE) AF: 0.472 AC: 32006 AN: 67880

Other (OTH) AF: 0.461 AC: 966 AN: 2094

Alfa AF: 0.459 Hom.: 45464

Bravo AF: 0.448

Asia WGS AF: 0.470 AC: 1630 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.3
DANN	Benign	0.67
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs857819; hg19: chr1-158734560;