Variant chr1-158777642-C-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 4P and 6B. PVS1_StrongBP6_ModerateBS2

The NM_001005278.2(OR6N2):c.-6-1G>T variant causes a splice acceptor change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00534 in 1,581,004 control chromosomes in the GnomAD database, including 26 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0037 ( 1 hom., cov: 32)

Exomes 𝑓: 0.0055 ( 25 hom. )

Consequence

OR6N2
NM_001005278.2 splice_acceptor

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.0250

Variant links:

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]

OR6N2 links:

OR6N1 (HGNC:):

OR6N1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

PVS1

Splicing variant, NOT destroyed by nmd, known LOF gene, truncates exone, which is 3.5838575 fraction of the gene.

BP6

Variant 1-158777642-C-A is Benign according to our data. Variant chr1-158777642-C-A is described in ClinVar as [Likely_benign]. Clinvar id is 2639480.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAdExome4 at 25 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE
OR6N2	NM_001005278.2 linkuse as main transcript	c.-6-1G>T	splice_acceptor_variant	ENST00000641131.1
OR6N1	XM_017000325.2 linkuse as main transcript	c.-193-5447G>T	intron_variant
OR6N1	XM_017000326.2 linkuse as main transcript	c.-194+3959G>T	intron_variant
OR6N1	XM_017000327.2 linkuse as main transcript	c.-193-5447G>T	intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
OR6N2	ENST00000641131.1 linkuse as main transcript	c.-6-1G>T		splice_acceptor_variant			NM_001005278.2	P1

Frequencies

GnomAD3 genomes

AF:

0.00366

AC:

557

AN:

152142

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00126

Gnomad AMI

AF:

0.0110

Gnomad AMR

AF:

0.00314

Gnomad ASJ

AF:

0.00518

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00186

Gnomad FIN

AF:

0.000377

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00598

Gnomad OTH

AF:

0.00430

GnomAD3 exomes

AF:

0.00399

AC:

938

AN:

235200

Hom.:

AF XY:

0.00412

AC XY:

528

AN XY:

128192

show subpopulations

Gnomad AFR exome

AF:

0.000870

Gnomad AMR exome

AF:

0.00185

Gnomad ASJ exome

AF:

0.00926

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00194

Gnomad FIN exome

AF:

0.00114

Gnomad NFE exome

AF:

0.00644

Gnomad OTH exome

AF:

0.00391

GnomAD4 exome

AF:

0.00552

AC:

7886

AN:

1428744

Hom.:

Cov.:

AF XY:

0.00540

AC XY:

3833

AN XY:

709764

show subpopulations

Gnomad4 AFR exome

AF:

0.000923

Gnomad4 AMR exome

AF:

0.00222

Gnomad4 ASJ exome

AF:

0.00826

Gnomad4 EAS exome

AF:

0.0000254

Gnomad4 SAS exome

AF:

0.00223

Gnomad4 FIN exome

AF:

0.00106

Gnomad4 NFE exome

AF:

0.00643

Gnomad4 OTH exome

AF:

0.00523

GnomAD4 genome

AF:

0.00366

AC:

557

AN:

152260

Hom.:

Cov.:

AF XY:

0.00340

AC XY:

253

AN XY:

74454

show subpopulations

Gnomad4 AFR

AF:

0.00125

Gnomad4 AMR

AF:

0.00314

Gnomad4 ASJ

AF:

0.00518

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00186

Gnomad4 FIN

AF:

0.000377

Gnomad4 NFE

AF:

0.00598

Gnomad4 OTH

AF:

0.00426

Alfa

AF:

0.00436

Hom.:

Bravo

AF:

0.00361

Asia WGS

AF:

0.000289

AC:

AN:

3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Nov 01, 2022

OR6N2: BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

DANN

Benign

0.67

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over