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. The variant received -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
• Publications: 5 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=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.862 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.870 AC: 36104 AN: 41518

American (AMR) AF: 0.449 AC: 6843 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.395 AC: 1371 AN: 3468

East Asian (EAS) AF: 0.610 AC: 3148 AN: 5164

South Asian (SAS) AF: 0.614 AC: 2962 AN: 4826

European-Finnish (FIN) AF: 0.385 AC: 4068 AN: 10558

Middle Eastern (MID) AF: 0.429 AC: 126 AN: 294

European-Non Finnish (NFE) AF: 0.351 AC: 23861 AN: 67948

Other (OTH) AF: 0.473 AC: 996 AN: 2106

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	6.0
DANN	Benign	0.79
PhyloP100		0.038

Splicing

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

Other links and lift over

dbSNP: rs857859; hg19: chr1-158771450;