11-4999404-G-T

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2

The NM_001004755.2(OR51L1):​c.422G>T​(p.Ser141Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000144 in 1,614,172 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/21 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: 𝑓 0.00072 ( 2 hom., cov: 32)
Exomes 𝑓: 0.000084 ( 0 hom. )

Consequence

OR51L1
NM_001004755.2 missense

Scores

2
17

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.489
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 Benign. Variant got -8 ACMG points.

BP4
Computational evidence support a benign effect (MetaRNN=0.0073967576).
BS2
High Homozygotes in GnomAd4 at 2 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
OR51L1NM_001004755.2 linkc.422G>T p.Ser141Ile 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.422G>T p.Ser141Ile missense_variant Exon 3 of 3 NM_001004755.2 ENSP00000493015.1 Q8NGJ5
OR51L1ENST00000641624.1 linkn.587+1821G>T intron_variant Intron 2 of 3
OR51L1ENST00000642056.1 linkn.587+1821G>T intron_variant Intron 2 of 2

Frequencies

GnomAD3 genomes
AF:
0.000723
AC:
110
AN:
152160
Hom.:
2
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.00261
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0000654
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000147
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.000235
AC:
59
AN:
251408
Hom.:
0
AF XY:
0.000155
AC XY:
21
AN XY:
135876
show subpopulations
Gnomad AFR exome
AF:
0.00320
Gnomad AMR exome
AF:
0.000145
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:
0.00000880
Gnomad OTH exome
AF:
0.000163
GnomAD4 exome
AF:
0.0000841
AC:
123
AN:
1461894
Hom.:
0
Cov.:
38
AF XY:
0.0000811
AC XY:
59
AN XY:
727248
show subpopulations
Gnomad4 AFR exome
AF:
0.00326
Gnomad4 AMR exome
AF:
0.000157
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000116
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
8.99e-7
Gnomad4 OTH exome
AF:
0.0000662
GnomAD4 genome
AF:
0.000722
AC:
110
AN:
152278
Hom.:
2
Cov.:
32
AF XY:
0.000712
AC XY:
53
AN XY:
74448
show subpopulations
Gnomad4 AFR
AF:
0.00260
Gnomad4 AMR
AF:
0.0000654
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000147
Gnomad4 OTH
AF:
0.00
Alfa
AF:
0.0000772
Hom.:
0
Bravo
AF:
0.000842
ESP6500AA
AF:
0.00318
AC:
14
ESP6500EA
AF:
0.00
AC:
0
ExAC
AF:
0.000231
AC:
28

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.13
BayesDel_addAF
Benign
-0.52
T
BayesDel_noAF
Benign
-0.53
CADD
Benign
14
DANN
Benign
0.96
DEOGEN2
Benign
0.0069
T;T
Eigen
Benign
-0.55
Eigen_PC
Benign
-0.70
FATHMM_MKL
Benign
0.19
N
LIST_S2
Benign
0.28
.;T
M_CAP
Benign
0.0067
T
MetaRNN
Benign
0.0074
T;T
MetaSVM
Benign
-1.0
T
MutationAssessor
Uncertain
2.4
M;M
PrimateAI
Benign
0.26
T
PROVEAN
Uncertain
-3.0
.;D
REVEL
Benign
0.052
Sift
Benign
0.051
.;T
Sift4G
Benign
0.083
.;T
Polyphen
0.80
P;P
Vest4
0.33
MVP
0.38
MPC
0.077
ClinPred
0.094
T
GERP RS
2.3
Varity_R
0.17
gMVP
0.29

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: rs140019286; hg19: chr11-5020634; API