rs857859

Variant names:

• chr1-158801660-T-A
• rs857859
• XM_017000325.2:c.-193-29465A>T

Your query was ambiguous. Multiple possible variants found:

• chr1-158801660-T-A
• chr1-158801660-T-C
• chr1-158801660-T-G

Variant summary

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

The XM_017000325.2(OR6N1):​c.-193-29465A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.525 in 152,050 control chromosomes in the GnomAD database, including 24,846 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 0.52 (24846 hom., cov: 31)
• Consequence: OR6N1 XM_017000325.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0380

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=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.862 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OR6N1	XM_017000325.2	c.-193-29465A>T		intron_variant	Intron 1 of 2		XP_016855814.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.524 AC: 79679 AN: 151932 Hom.: 24771 Cov.: 31

Gnomad AFR AF: 0.869

Gnomad AMI AF: 0.376

Gnomad AMR AF: 0.447

Gnomad ASJ AF: 0.395

Gnomad EAS AF: 0.611

Gnomad SAS AF: 0.613

Gnomad FIN AF: 0.385

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.351

Gnomad OTH AF: 0.466

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

GnomAD4 genome AF: 0.525 AC: 79822 AN: 152050 Hom.: 24846 Cov.: 31 AF XY: 0.528 AC XY: 39233 AN XY: 74338

Gnomad4 AFR AF: 0.870

Gnomad4 AMR AF: 0.449

Gnomad4 ASJ AF: 0.395

Gnomad4 EAS AF: 0.610

Gnomad4 SAS AF: 0.614

Gnomad4 FIN AF: 0.385

Gnomad4 NFE AF: 0.351

Gnomad4 OTH AF: 0.473

Alfa AF: 0.439 Hom.: 2062

Bravo AF: 0.541

Asia WGS AF: 0.648 AC: 2255 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	6.0
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs857859; hg19: chr1-158771450;