rs857838

Positions:

• chr1-158780760-A-C
• chr1-158780760-A-T

Variant summary

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

The NM_001005278.2(OR6N2):​c.-7+410T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.64 in 152,038 control chromosomes in the GnomAD database, including 31,749 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 0.64 (31749 hom., cov: 32)
• Consequence: OR6N2 NM_001005278.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0420

Genes affected

OR6N2 (HGNC:15035): (olfactory receptor family 6 subfamily N member 2) 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]

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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.769 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OR6N2	NM_001005278.2	c.-7+410T>G		intron_variant		ENST00000641131.1	NP_001005278.1
OR6N1	XM_017000325.2	c.-193-8565T>G		intron_variant			XP_016855814.1
OR6N1	XM_017000326.2	c.-194+841T>G		intron_variant			XP_016855815.1
OR6N1	XM_017000327.2	c.-194+3237T>G		intron_variant			XP_016855816.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OR6N2	ENST00000641131.1	c.-7+410T>G		intron_variant			NM_001005278.2	ENSP00000493148.1

Frequencies

GnomAD3 genomes AF: 0.639 AC: 97151 AN: 151920 Hom.: 31701 Cov.: 32

Gnomad AFR AF: 0.776

Gnomad AMI AF: 0.571

Gnomad AMR AF: 0.642

Gnomad ASJ AF: 0.615

Gnomad EAS AF: 0.639

Gnomad SAS AF: 0.702

Gnomad FIN AF: 0.548

Gnomad MID AF: 0.652

Gnomad NFE AF: 0.568

Gnomad OTH AF: 0.627

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

GnomAD4 genome AF: 0.640 AC: 97264 AN: 152038 Hom.: 31749 Cov.: 32 AF XY: 0.642 AC XY: 47703 AN XY: 74318

Gnomad4 AFR AF: 0.776

Gnomad4 AMR AF: 0.643

Gnomad4 ASJ AF: 0.615

Gnomad4 EAS AF: 0.638

Gnomad4 SAS AF: 0.704

Gnomad4 FIN AF: 0.548

Gnomad4 NFE AF: 0.568

Gnomad4 OTH AF: 0.632

Alfa AF: 0.587 Hom.: 41210

Bravo AF: 0.650

Asia WGS AF: 0.675 AC: 2347 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.8
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs857838; hg19: chr1-158750550;