rs1864346

Positions:

• chr1-158766655-C-A
• chr1-158766655-C-G
• chr1-158766655-C-T

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001005185.2(OR6N1):​c.28G>T​(p.Ala10Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A10T) has been classified as Likely benign.

• Frequency: Genomes: not found (cov: 31)
• Consequence: OR6N1 NM_001005185.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0710

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 Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.0402402).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
OR6N1	NM_001005185.2	c.28G>T	p.Ala10Ser	missense_variant	2/2	ENST00000641846.1
OR6N1	XM_017000325.2	c.28G>T	p.Ala10Ser	missense_variant	3/3
OR6N1	XM_017000326.2	c.28G>T	p.Ala10Ser	missense_variant	4/4
OR6N1	XM_017000327.2	c.28G>T	p.Ala10Ser	missense_variant	3/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
OR6N1	ENST00000641846.1	c.28G>T	p.Ala10Ser	missense_variant	2/2		NM_001005185.2	P1
OR6N1	ENST00000641189.1	n.175+5366G>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Cov.: 36

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.069
BayesDel_addAF	Benign	-0.35	T
BayesDel_noAF	Benign	-0.74
CADD	Benign	3.1
DANN	Benign	0.95
DEOGEN2	Benign	0.0020	T;T
Eigen	Benign	-1.1
Eigen_PC	Benign	-0.89
FATHMM_MKL	Benign	0.077	N
LIST_S2	Benign	0.033	.;T
M_CAP	Benign	0.0011	T
MetaRNN	Benign	0.040	T;T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	-0.97	N;N
MutationTaster	Benign	1.0	P
PrimateAI	Benign	0.28	T
PROVEAN	Benign	0.95	.;N
REVEL	Benign	0.017
Sift	Benign	0.18	.;T
Sift4G	Benign	0.25	.;T
Polyphen		0.0010	B;B
Vest4		0.040
MutPred		0.46		Gain of glycosylation at A10 (P = 0.0269);Gain of glycosylation at A10 (P = 0.0269);
MVP		0.24
MPC		0.025
ClinPred		0.16	T
GERP RS		2.5
Varity_R		0.033
gMVP		0.074

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.070		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs1864346; hg19: chr1-158736445;