chr15-101922950-A-G

Variant summary

Our verdict is Likely benign. Variant got -1 ACMG points: 0P and 1B. BP4

The ENST00000650172.1(OR4F4):ā€‹c.164T>Cā€‹(p.Leu55Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā˜…).

Frequency

Genomes: š‘“ 0.00047 ( 0 hom., cov: 15)
Exomes š‘“: 0.000077 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

OR4F4
ENST00000650172.1 missense

Scores

3
3
13

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 0.234
Variant links:
Genes affected
OR4F4 (HGNC:8301): (olfactory receptor family 4 subfamily F member 4) 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 -1 ACMG points.

BP4
Computational evidence support a benign effect (MetaRNN=0.3068649).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
OR4F4ENST00000650172.1 linkuse as main transcriptc.164T>C p.Leu55Pro missense_variant 1/1 P1

Frequencies

GnomAD3 genomes
AF:
0.00
AC:
52
AN:
110334
Hom.:
0
Cov.:
15
FAILED QC
Gnomad AFR
AF:
0.00211
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000354
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:
0.00
Gnomad OTH
AF:
0.00
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
AF:
0.0000772
AC:
37
AN:
479044
Hom.:
0
Cov.:
5
AF XY:
0.0000474
AC XY:
12
AN XY:
253300
show subpopulations
Gnomad4 AFR exome
AF:
0.00252
Gnomad4 AMR exome
AF:
0.000103
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000218
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.000111
GnomAD4 genome
Data not reliable, filtered out with message: AS_VQSR
AF:
0.000471
AC:
52
AN:
110430
Hom.:
0
Cov.:
15
AF XY:
0.000500
AC XY:
26
AN XY:
52016
show subpopulations
Gnomad4 AFR
AF:
0.00210
Gnomad4 AMR
AF:
0.000353
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00
Gnomad4 OTH
AF:
0.00
Alfa
AF:
0.000253
Hom.:
0

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 24, 2022The c.110T>C (p.L37P) alteration is located in exon 1 (coding exon 1) of the OR4F4 gene. This alteration results from a T to C substitution at nucleotide position 110, causing the leucine (L) at amino acid position 37 to be replaced by a proline (P). 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
Uncertain
0.54
BayesDel_addAF
Benign
-0.21
T
BayesDel_noAF
Benign
-0.54
CADD
Uncertain
24
DANN
Benign
0.88
DEOGEN2
Benign
0.14
T;.
Eigen
Benign
-0.64
Eigen_PC
Benign
-0.81
FATHMM_MKL
Benign
0.082
N
LIST_S2
Uncertain
0.92
D;D
M_CAP
Benign
0.00069
T
MetaRNN
Benign
0.31
T;T
MetaSVM
Benign
-1.0
T
MutationAssessor
Pathogenic
3.4
M;.
MutationTaster
Benign
1.0
N
PrimateAI
Benign
0.42
T
PROVEAN
Pathogenic
-5.8
D;.
REVEL
Benign
0.057
Sift
Uncertain
0.013
D;.
Sift4G
Pathogenic
0.0
D;.
Polyphen
0.0040
B;.
Vest4
0.45
MutPred
0.76
Loss of stability (P = 0.0664);.;
MVP
0.21
ClinPred
0.22
T
GERP RS
1.8
Varity_R
0.75
gMVP
0.35

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.030
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: rs1432524753; hg19: chr15-102463153; API