11-4999019-A-G

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_001004755.2(OR51L1):​c.37A>G​(p.Ile13Val) 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.

Frequency

Genomes: not found (cov: 32)
Exomes š‘“: 6.8e-7 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

OR51L1
NM_001004755.2 missense

Scores

19

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.126
Variant links:
Genes affected
OR51L1 (HGNC:14759): (olfactory receptor family 51 subfamily L 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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

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=0.03595987).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
OR51L1NM_001004755.2 linkc.37A>G p.Ile13Val missense_variant Exon 3 of 3 ENST00000641819.1 NP_001004755.1 Q8NGJ5A0A126GVJ8

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
OR51L1ENST00000641819.1 linkc.37A>G p.Ile13Val missense_variant Exon 3 of 3 NM_001004755.2 ENSP00000493015.1 Q8NGJ5
OR51L1ENST00000641624.1 linkn.587+1436A>G intron_variant Intron 2 of 3
OR51L1ENST00000642056.1 linkn.587+1436A>G intron_variant Intron 2 of 2

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD3 exomes
AF:
0.00000398
AC:
1
AN:
251228
Hom.:
0
AF XY:
0.00
AC XY:
0
AN XY:
135776
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.0000289
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
AF:
6.84e-7
AC:
1
AN:
1461740
Hom.:
0
Cov.:
33
AF XY:
0.00
AC XY:
0
AN XY:
727180
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.0000224
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.065
BayesDel_addAF
Benign
-0.42
T
BayesDel_noAF
Benign
-0.75
CADD
Benign
0.062
DANN
Benign
0.66
DEOGEN2
Benign
0.00042
T;T
Eigen
Benign
-0.92
Eigen_PC
Benign
-0.81
FATHMM_MKL
Benign
0.058
N
LIST_S2
Benign
0.11
.;T
M_CAP
Benign
0.00074
T
MetaRNN
Benign
0.036
T;T
MetaSVM
Benign
-0.96
T
MutationAssessor
Benign
0.030
N;N
PrimateAI
Benign
0.23
T
PROVEAN
Benign
0.22
.;N
REVEL
Benign
0.032
Sift
Benign
0.33
.;T
Sift4G
Benign
0.49
.;T
Polyphen
0.0020
B;B
Vest4
0.045
MutPred
0.29
Gain of methylation at R17 (P = 0.1883);Gain of methylation at R17 (P = 0.1883);
MVP
0.17
MPC
0.030
ClinPred
0.057
T
GERP RS
0.67
Varity_R
0.024
gMVP
0.028

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
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.

Other links and lift over

dbSNP: rs927399811; hg19: chr11-5020249; COSMIC: COSV58626026; API