11-5200445-T-G
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Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_001004760.3(OR51V1):āc.238A>Cā(p.Thr80Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000511 in 1,613,824 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Genomes: š 0.00026 ( 0 hom., cov: 31)
Exomes š: 0.00054 ( 2 hom. )
Consequence
OR51V1
NM_001004760.3 missense
NM_001004760.3 missense
Scores
3
4
12
Clinical Significance
Conservation
PhyloP100: 0.863
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]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -6 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=0.18622124).
BS2
High Homozygotes in GnomAdExome4 at 2 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
OR51V1 | NM_001004760.3 | c.238A>C | p.Thr80Pro | missense_variant | 1/1 | ENST00000641270.1 | NP_001004760.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
OR51V1 | ENST00000641270.1 | c.238A>C | p.Thr80Pro | missense_variant | 1/1 | NM_001004760.3 | ENSP00000492968 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000263 AC: 40AN: 151856Hom.: 0 Cov.: 31
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GnomAD3 exomes AF: 0.000263 AC: 66AN: 250976Hom.: 0 AF XY: 0.000258 AC XY: 35AN XY: 135608
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GnomAD4 exome AF: 0.000537 AC: 785AN: 1461850Hom.: 2 Cov.: 40 AF XY: 0.000528 AC XY: 384AN XY: 727230
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GnomAD4 genome AF: 0.000263 AC: 40AN: 151974Hom.: 0 Cov.: 31 AF XY: 0.000242 AC XY: 18AN XY: 74290
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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 submitter | clinical testing | Ambry Genetics | Aug 11, 2022 | The c.256A>C (p.T86P) alteration is located in exon 1 (coding exon 1) of the OR51V1 gene. This alteration results from a A to C substitution at nucleotide position 256, causing the threonine (T) at amino acid position 86 to be replaced by a proline (P). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Uncertain
CADD
Benign
DANN
Uncertain
DEOGEN2
Benign
.;T
Eigen
Uncertain
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T;T
M_CAP
Benign
T
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationAssessor
Pathogenic
.;H
MutationTaster
Benign
N
PrimateAI
Benign
T
PROVEAN
Pathogenic
.;D
REVEL
Benign
Sift
Uncertain
.;D
Sift4G
Pathogenic
.;D
Polyphen
1.0
.;D
Vest4
0.63
MVP
0.47
ClinPred
T
GERP RS
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gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at