rs28545014

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001001918.1(OR14C36):​c.691G>T​(p.Asp231Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.546 in 1,613,194 control chromosomes in the GnomAD database, including 242,214 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.50 ( 19768 hom., cov: 31)
Exomes 𝑓: 0.55 ( 222446 hom. )

Consequence

OR14C36
NM_001001918.1 missense

Scores

4
14

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.121
Variant links:
Genes affected
OR14C36 (HGNC:15026): (olfactory receptor family 14 subfamily C member 36) 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 -12 ACMG points.

BP4
Computational evidence support a benign effect (MetaRNN=1.3116002E-4).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.554 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
OR14C36NM_001001918.1 linkuse as main transcriptc.691G>T p.Asp231Tyr missense_variant 1/1 ENST00000317861.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
OR14C36ENST00000317861.1 linkuse as main transcriptc.691G>T p.Asp231Tyr missense_variant 1/1 NM_001001918.1 P1

Frequencies

GnomAD3 genomes
AF:
0.505
AC:
76550
AN:
151708
Hom.:
19760
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.401
Gnomad AMI
AF:
0.729
Gnomad AMR
AF:
0.492
Gnomad ASJ
AF:
0.544
Gnomad EAS
AF:
0.424
Gnomad SAS
AF:
0.538
Gnomad FIN
AF:
0.565
Gnomad MID
AF:
0.544
Gnomad NFE
AF:
0.559
Gnomad OTH
AF:
0.519
GnomAD3 exomes
AF:
0.525
AC:
131364
AN:
250396
Hom.:
34857
AF XY:
0.533
AC XY:
72145
AN XY:
135326
show subpopulations
Gnomad AFR exome
AF:
0.393
Gnomad AMR exome
AF:
0.467
Gnomad ASJ exome
AF:
0.546
Gnomad EAS exome
AF:
0.422
Gnomad SAS exome
AF:
0.526
Gnomad FIN exome
AF:
0.562
Gnomad NFE exome
AF:
0.567
Gnomad OTH exome
AF:
0.551
GnomAD4 exome
AF:
0.550
AC:
803694
AN:
1461368
Hom.:
222446
Cov.:
50
AF XY:
0.550
AC XY:
399768
AN XY:
727004
show subpopulations
Gnomad4 AFR exome
AF:
0.400
Gnomad4 AMR exome
AF:
0.469
Gnomad4 ASJ exome
AF:
0.546
Gnomad4 EAS exome
AF:
0.428
Gnomad4 SAS exome
AF:
0.530
Gnomad4 FIN exome
AF:
0.566
Gnomad4 NFE exome
AF:
0.563
Gnomad4 OTH exome
AF:
0.545
GnomAD4 genome
AF:
0.505
AC:
76597
AN:
151826
Hom.:
19768
Cov.:
31
AF XY:
0.505
AC XY:
37508
AN XY:
74204
show subpopulations
Gnomad4 AFR
AF:
0.401
Gnomad4 AMR
AF:
0.491
Gnomad4 ASJ
AF:
0.544
Gnomad4 EAS
AF:
0.424
Gnomad4 SAS
AF:
0.540
Gnomad4 FIN
AF:
0.565
Gnomad4 NFE
AF:
0.559
Gnomad4 OTH
AF:
0.518
Alfa
AF:
0.545
Hom.:
35724
Bravo
AF:
0.495
TwinsUK
AF:
0.556
AC:
2060
ALSPAC
AF:
0.564
AC:
2175
ESP6500AA
AF:
0.401
AC:
1768
ESP6500EA
AF:
0.569
AC:
4894
ExAC
AF:
0.526
AC:
63877
Asia WGS
AF:
0.479
AC:
1662
AN:
3478
EpiCase
AF:
0.558
EpiControl
AF:
0.566

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.14
BayesDel_addAF
Benign
-0.76
T
BayesDel_noAF
Benign
-0.72
CADD
Benign
19
DANN
Uncertain
0.99
DEOGEN2
Benign
0.0085
T
Eigen
Benign
-0.24
Eigen_PC
Benign
-0.44
FATHMM_MKL
Benign
0.033
N
LIST_S2
Benign
0.37
T
MetaRNN
Benign
0.00013
T
MetaSVM
Benign
-1.1
T
MutationAssessor
Benign
1.9
L
MutationTaster
Benign
1.0
P
PrimateAI
Benign
0.24
T
PROVEAN
Uncertain
-3.6
D
REVEL
Benign
0.082
Sift
Uncertain
0.0080
D
Sift4G
Uncertain
0.0030
D
Polyphen
1.0
D
Vest4
0.079
MPC
0.70
ClinPred
0.022
T
GERP RS
1.6
Varity_R
0.68
gMVP
0.23

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.020
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: rs28545014; hg19: chr1-248512767; COSMIC: COSV58600667; API