chr11-5200469-T-C

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_001004760.3(OR51V1):ā€‹c.214A>Gā€‹(p.Thr72Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000181 in 1,613,562 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā˜…).

Frequency

Genomes: š‘“ 0.00011 ( 0 hom., cov: 31)
Exomes š‘“: 0.00019 ( 0 hom. )

Consequence

OR51V1
NM_001004760.3 missense

Scores

3
16

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: -0.181
Variant links:
Genes affected
OR51V1 (HGNC:19597): (olfactory receptor family 51 subfamily V 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 Uncertain_significance. Variant got 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.1627506).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
OR51V1NM_001004760.3 linkuse as main transcriptc.214A>G p.Thr72Ala missense_variant 1/1 ENST00000641270.1 NP_001004760.3

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
OR51V1ENST00000641270.1 linkuse as main transcriptc.214A>G p.Thr72Ala missense_variant 1/1 NM_001004760.3 ENSP00000492968 P1

Frequencies

GnomAD3 genomes
AF:
0.000105
AC:
16
AN:
151744
Hom.:
0
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.0000969
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
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:
0.000177
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.0000957
AC:
24
AN:
250898
Hom.:
0
AF XY:
0.0000885
AC XY:
12
AN XY:
135554
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
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:
0.000203
Gnomad OTH exome
AF:
0.000164
GnomAD4 exome
AF:
0.000189
AC:
276
AN:
1461818
Hom.:
0
Cov.:
40
AF XY:
0.000175
AC XY:
127
AN XY:
727204
show subpopulations
Gnomad4 AFR exome
AF:
0.000119
Gnomad4 AMR exome
AF:
0.00
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:
0.000234
Gnomad4 OTH exome
AF:
0.000199
GnomAD4 genome
AF:
0.000105
AC:
16
AN:
151744
Hom.:
0
Cov.:
31
AF XY:
0.000135
AC XY:
10
AN XY:
74100
show subpopulations
Gnomad4 AFR
AF:
0.0000969
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000177
Gnomad4 OTH
AF:
0.00
Alfa
AF:
0.000156
Hom.:
0
Bravo
AF:
0.0000907
TwinsUK
AF:
0.000270
AC:
1
ALSPAC
AF:
0.000259
AC:
1
ESP6500AA
AF:
0.00
AC:
0
ESP6500EA
AF:
0.000116
AC:
1
ExAC
AF:
0.0000741
AC:
9
EpiCase
AF:
0.000218
EpiControl
AF:
0.000119

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingAmbry GeneticsJan 30, 2024The c.232A>G (p.T78A) alteration is located in exon 1 (coding exon 1) of the OR51V1 gene. This alteration results from a A to G substitution at nucleotide position 232, causing the threonine (T) at amino acid position 78 to be replaced by an alanine (A). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.13
BayesDel_addAF
Benign
-0.47
T
BayesDel_noAF
Benign
-0.61
CADD
Benign
19
DANN
Uncertain
0.99
DEOGEN2
Benign
0.0082
.;T
Eigen
Benign
0.032
Eigen_PC
Benign
-0.097
FATHMM_MKL
Benign
0.17
N
LIST_S2
Benign
0.79
T;T
M_CAP
Benign
0.0051
T
MetaRNN
Benign
0.16
T;T
MetaSVM
Benign
-1.1
T
MutationAssessor
Benign
1.3
.;L
MutationTaster
Benign
1.0
N
PrimateAI
Benign
0.21
T
PROVEAN
Uncertain
-4.2
.;D
REVEL
Benign
0.069
Sift
Uncertain
0.0080
.;D
Sift4G
Benign
0.063
.;T
Polyphen
1.0
.;D
Vest4
0.28
MVP
0.29
ClinPred
0.33
T
GERP RS
4.1
Varity_R
0.34
gMVP
0.064

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.

Other links and lift over

dbSNP: rs201525999; hg19: chr11-5221699; API