Variant 9-122750491-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001004453.3(OR1L6):c.644T>C(p.Ile215Thr) variant causes a missense change. 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 0.89 ( 53140 hom., cov: 16)

Exomes 𝑓: 0.92 ( 373455 hom. )

Consequence

OR1L6
NM_001004453.3 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 4.83

Variant links:

Genes affected

OR1L6 (HGNC:8218): (olfactory receptor family 1 subfamily L member 6) 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]

OR1L6 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=9.5023984E-7).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.974 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OR1L6	NM_001004453.3 link	c.644T>C	p.Ile215Thr	missense_variant	2/2	ENST00000304720.3	NP_001004453.2	Q8NGR2A0A0C4DFP2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OR1L6	ENST00000304720.3 link	c.644T>C	p.Ile215Thr	missense_variant	2/2	6	NM_001004453.3	ENSP00000304235.2		A0A0C4DFP2
OR1L6	ENST00000373684.1 link	c.752T>C	p.Ile251Thr	missense_variant	1/1	6		ENSP00000362788.1		Q8NGR2

Frequencies

GnomAD3 genomes

AF:

0.895

AC:

117061

AN:

130832

Hom.:

53138

Cov.:

show subpopulations

Gnomad AFR

AF:

0.735

Gnomad AMI

AF:

0.893

Gnomad AMR

AF:

0.946

Gnomad ASJ

AF:

0.955

Gnomad EAS

AF:

0.999

Gnomad SAS

AF:

0.943

Gnomad FIN

AF:

0.893

Gnomad MID

AF:

0.952

Gnomad NFE

AF:

0.962

Gnomad OTH

AF:

0.926

GnomAD3 exomes

AF:

0.899

AC:

171260

AN:

190408

Hom.:

83693

AF XY:

0.902

AC XY:

91463

AN XY:

101368

show subpopulations

Gnomad AFR exome

AF:

0.611

Gnomad AMR exome

AF:

0.962

Gnomad ASJ exome

AF:

0.901

Gnomad EAS exome

AF:

0.998

Gnomad SAS exome

AF:

0.904

Gnomad FIN exome

AF:

0.809

Gnomad NFE exome

AF:

0.919

Gnomad OTH exome

AF:

0.913

GnomAD4 exome

AF:

0.922

AC:

767176

AN:

832052

Hom.:

373455

Cov.:

AF XY:

0.925

AC XY:

400011

AN XY:

432604

show subpopulations

Gnomad4 AFR exome

AF:

0.651

Gnomad4 AMR exome

AF:

0.968

Gnomad4 ASJ exome

AF:

0.941

Gnomad4 EAS exome

AF:

0.999

Gnomad4 SAS exome

AF:

0.932

Gnomad4 FIN exome

AF:

0.905

Gnomad4 NFE exome

AF:

0.925

Gnomad4 OTH exome

AF:

0.916

GnomAD4 genome

AF:

0.894

AC:

117093

AN:

130924

Hom.:

53140

Cov.:

AF XY:

0.892

AC XY:

55586

AN XY:

62306

show subpopulations

Gnomad4 AFR

AF:

0.734

Gnomad4 AMR

AF:

0.946

Gnomad4 ASJ

AF:

0.955

Gnomad4 EAS

AF:

0.999

Gnomad4 SAS

AF:

0.943

Gnomad4 FIN

AF:

0.893

Gnomad4 NFE

AF:

0.962

Gnomad4 OTH

AF:

0.925

Alfa

AF:

0.919

Hom.:

12590

Bravo

AF:

0.899

ExAC

AF:

0.876

AC:

104783

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Uncertain

0.39

BayesDel_addAF

Benign

-0.59

BayesDel_noAF

Benign

-0.48

CADD

Uncertain

DANN

Uncertain

1.0

DEOGEN2

Benign

0.019

.;T

Eigen

Uncertain

0.24

Eigen_PC

Benign

0.18

FATHMM_MKL

Benign

0.54

LIST_S2

Benign

0.68

T;T

MetaRNN

Benign

9.5e-7

T;T

MetaSVM

Benign

-0.89

MutationAssessor

Benign

1.7

.;L

PrimateAI

Benign

0.30

PROVEAN

Pathogenic

-4.8

D;D

REVEL

Benign

0.13

Sift

Uncertain

0.012

D;D

Sift4G

Uncertain

0.010

D;D

Polyphen

0.96

.;D

Vest4

0.29

MPC

0.40

ClinPred

0.069

GERP RS

3.4

Varity_R

0.34

gMVP

0.17

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

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

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over