11-5200078-G-T

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The NM_001004760.3(OR51V1):​c.605C>A​(p.Ala202Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00091 in 1,612,584 control chromosomes in the GnomAD database, including 2 homozygotes. 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 (★).

Frequency

Genomes: 𝑓 0.00061 ( 1 hom., cov: 32)
Exomes 𝑓: 0.00094 ( 1 hom. )

Consequence

OR51V1
NM_001004760.3 missense

Scores

2
2
15

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: -0.188
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 Likely_benign. Variant got -4 ACMG points.

BP4
Computational evidence support a benign effect (MetaRNN=0.038325965).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
OR51V1NM_001004760.3 linkuse as main transcriptc.605C>A p.Ala202Asp 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.605C>A p.Ala202Asp missense_variant 1/1 NM_001004760.3 ENSP00000492968 P1

Frequencies

GnomAD3 genomes
AF:
0.000611
AC:
93
AN:
152096
Hom.:
1
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.000290
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000131
Gnomad ASJ
AF:
0.000289
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.000377
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00109
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.000571
AC:
143
AN:
250458
Hom.:
0
AF XY:
0.000561
AC XY:
76
AN XY:
135380
show subpopulations
Gnomad AFR exome
AF:
0.000123
Gnomad AMR exome
AF:
0.0000289
Gnomad ASJ exome
AF:
0.000697
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.000231
Gnomad NFE exome
AF:
0.00110
Gnomad OTH exome
AF:
0.000654
GnomAD4 exome
AF:
0.000941
AC:
1374
AN:
1460370
Hom.:
1
Cov.:
30
AF XY:
0.000941
AC XY:
684
AN XY:
726524
show subpopulations
Gnomad4 AFR exome
AF:
0.000120
Gnomad4 AMR exome
AF:
0.000112
Gnomad4 ASJ exome
AF:
0.000306
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.000374
Gnomad4 NFE exome
AF:
0.00118
Gnomad4 OTH exome
AF:
0.000464
GnomAD4 genome
AF:
0.000611
AC:
93
AN:
152214
Hom.:
1
Cov.:
32
AF XY:
0.000591
AC XY:
44
AN XY:
74420
show subpopulations
Gnomad4 AFR
AF:
0.000289
Gnomad4 AMR
AF:
0.000131
Gnomad4 ASJ
AF:
0.000289
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.000377
Gnomad4 NFE
AF:
0.00109
Gnomad4 OTH
AF:
0.00
Alfa
AF:
0.000903
Hom.:
0
Bravo
AF:
0.000514
TwinsUK
AF:
0.000270
AC:
1
ALSPAC
AF:
0.00130
AC:
5
ESP6500AA
AF:
0.000227
AC:
1
ESP6500EA
AF:
0.00116
AC:
10
ExAC
AF:
0.000511
AC:
62
EpiCase
AF:
0.00153
EpiControl
AF:
0.000830

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 GeneticsJun 11, 2021The c.623C>A (p.A208D) alteration is located in exon 1 (coding exon 1) of the OR51V1 gene. This alteration results from a C to A substitution at nucleotide position 623, causing the alanine (A) at amino acid position 208 to be replaced by an aspartic acid (D). 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
Pathogenic
0.68
BayesDel_addAF
Benign
-0.33
T
BayesDel_noAF
Benign
-0.28
CADD
Benign
18
DANN
Uncertain
0.97
DEOGEN2
Benign
0.0027
.;T
Eigen
Benign
-0.44
Eigen_PC
Benign
-0.65
FATHMM_MKL
Benign
0.12
N
LIST_S2
Benign
0.77
T;T
M_CAP
Benign
0.026
D
MetaRNN
Benign
0.038
T;T
MetaSVM
Benign
-0.87
T
MutationAssessor
Benign
1.0
.;L
MutationTaster
Benign
1.0
N
PrimateAI
Benign
0.20
T
PROVEAN
Benign
-1.8
.;N
REVEL
Benign
0.25
Sift
Uncertain
0.0020
.;D
Sift4G
Pathogenic
0.0010
.;D
Polyphen
1.0
.;D
Vest4
0.39
MVP
0.17
ClinPred
0.073
T
GERP RS
-0.47
Varity_R
0.58
gMVP
0.50

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: rs148749797; hg19: chr11-5221308; API