rs857819

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OR6N1	NM_001005185.2	c.*974G>A		3_prime_UTR_variant	Exon 2 of 2	ENST00000641846.1	NP_001005185.1
OR6N1	XM_017000325.2	c.*974G>A		3_prime_UTR_variant	Exon 3 of 3		XP_016855814.1
OR6N1	XM_017000326.2	c.*974G>A		3_prime_UTR_variant	Exon 4 of 4		XP_016855815.1
OR6N1	XM_017000327.2	c.*974G>A		3_prime_UTR_variant	Exon 3 of 3		XP_016855816.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OR6N1	ENST00000641846	c.*974G>A		3_prime_UTR_variant	Exon 2 of 2		NM_001005185.2	ENSP00000493254.1
OR6N1	ENST00000641189.1	n.175+7251G>A		intron_variant	Intron 1 of 1

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

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

Gnomad4 AFR AF: 0.321

Gnomad4 AMR AF: 0.564

Gnomad4 ASJ AF: 0.439

Gnomad4 EAS AF: 0.605

Gnomad4 SAS AF: 0.269

Gnomad4 FIN AF: 0.475

Gnomad4 NFE AF: 0.472

Gnomad4 OTH AF: 0.461

Alfa AF: 0.458 Hom.: 18807

Bravo AF: 0.448

Asia WGS AF: 0.470 AC: 1630 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs857819; hg19: chr1-158734560;