rs10838851

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_001004726.1(OR4X1):​c.819T>A​(p.Tyr273Ter) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.731 in 1,613,266 control chromosomes in the GnomAD database, including 435,620 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.69 ( 36959 hom., cov: 33)
Exomes 𝑓: 0.73 ( 398661 hom. )

Consequence

OR4X1
NM_001004726.1 stop_gained

Scores

1
2
4

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.25
Variant links:
Genes affected
OR4X1 (HGNC:14854): (olfactory receptor family 4 subfamily X 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. This olfactory receptor gene is a segregating pseudogene, where some individuals have an allele that encodes a functional olfactory receptor, while other individuals have an allele encoding a protein that is predicted to be non-functional. [provided by RefSeq, Jul 2015]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.751 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
OR4X1NM_001004726.1 linkuse as main transcriptc.819T>A p.Tyr273Ter stop_gained 1/1 ENST00000320048.1 NP_001004726.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
OR4X1ENST00000320048.1 linkuse as main transcriptc.819T>A p.Tyr273Ter stop_gained 1/1 NM_001004726.1 ENSP00000321506 P1

Frequencies

GnomAD3 genomes
AF:
0.690
AC:
104863
AN:
152022
Hom.:
36946
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.559
Gnomad AMI
AF:
0.836
Gnomad AMR
AF:
0.737
Gnomad ASJ
AF:
0.693
Gnomad EAS
AF:
0.577
Gnomad SAS
AF:
0.544
Gnomad FIN
AF:
0.811
Gnomad MID
AF:
0.680
Gnomad NFE
AF:
0.757
Gnomad OTH
AF:
0.679
GnomAD3 exomes
AF:
0.710
AC:
178267
AN:
250956
Hom.:
64742
AF XY:
0.701
AC XY:
94996
AN XY:
135606
show subpopulations
Gnomad AFR exome
AF:
0.556
Gnomad AMR exome
AF:
0.808
Gnomad ASJ exome
AF:
0.696
Gnomad EAS exome
AF:
0.581
Gnomad SAS exome
AF:
0.532
Gnomad FIN exome
AF:
0.799
Gnomad NFE exome
AF:
0.756
Gnomad OTH exome
AF:
0.717
GnomAD4 exome
AF:
0.735
AC:
1073912
AN:
1461126
Hom.:
398661
Cov.:
40
AF XY:
0.729
AC XY:
530178
AN XY:
726918
show subpopulations
Gnomad4 AFR exome
AF:
0.550
Gnomad4 AMR exome
AF:
0.800
Gnomad4 ASJ exome
AF:
0.692
Gnomad4 EAS exome
AF:
0.628
Gnomad4 SAS exome
AF:
0.541
Gnomad4 FIN exome
AF:
0.793
Gnomad4 NFE exome
AF:
0.757
Gnomad4 OTH exome
AF:
0.700
GnomAD4 genome
AF:
0.690
AC:
104914
AN:
152140
Hom.:
36959
Cov.:
33
AF XY:
0.689
AC XY:
51251
AN XY:
74382
show subpopulations
Gnomad4 AFR
AF:
0.559
Gnomad4 AMR
AF:
0.737
Gnomad4 ASJ
AF:
0.693
Gnomad4 EAS
AF:
0.578
Gnomad4 SAS
AF:
0.545
Gnomad4 FIN
AF:
0.811
Gnomad4 NFE
AF:
0.757
Gnomad4 OTH
AF:
0.679
Alfa
AF:
0.735
Hom.:
13412
Bravo
AF:
0.682
TwinsUK
AF:
0.767
AC:
2845
ALSPAC
AF:
0.766
AC:
2951
ESP6500AA
AF:
0.566
AC:
2491
ESP6500EA
AF:
0.755
AC:
6486
ExAC
AF:
0.704
AC:
85411
Asia WGS
AF:
0.514
AC:
1787
AN:
3476
EpiCase
AF:
0.738
EpiControl
AF:
0.729

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Uncertain
0.14
D
BayesDel_noAF
Pathogenic
0.57
CADD
Pathogenic
34
DANN
Uncertain
0.98
Eigen
Benign
-0.014
Eigen_PC
Benign
-0.29
FATHMM_MKL
Benign
0.22
N
MutationTaster
Benign
0.000027
P
Vest4
0.12
GERP RS
2.4

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: rs10838851; hg19: chr11-48286231; COSMIC: COSV60723080; API