chr6-29173679-T-C
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Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_030905.3(OR2J2):āc.44T>Cā(p.Leu15Pro) variant causes a missense change. The variant allele was found at a frequency of 0.00000806 in 1,612,582 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Genomes: š 0.0000066 ( 0 hom., cov: 31)
Exomes š: 0.0000082 ( 0 hom. )
Consequence
OR2J2
NM_030905.3 missense
NM_030905.3 missense
Scores
3
3
10
Clinical Significance
Conservation
PhyloP100: 4.00
Genes affected
OR2J2 (HGNC:8260): (olfactory receptor family 2 subfamily J member 2) 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 Uncertain_significance. Variant got 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
OR2J2 | NM_030905.3 | c.44T>C | p.Leu15Pro | missense_variant | 2/2 | ENST00000641417.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OR2J2 | ENST00000641417.1 | c.44T>C | p.Leu15Pro | missense_variant | 2/2 | NM_030905.3 | P1 | ||
OR2J2 | ENST00000377167.3 | c.44T>C | p.Leu15Pro | missense_variant | 1/1 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 152016Hom.: 0 Cov.: 31
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GnomAD3 exomes AF: 0.0000121 AC: 3AN: 247900Hom.: 0 AF XY: 0.0000149 AC XY: 2AN XY: 134530
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GnomAD4 exome AF: 0.00000822 AC: 12AN: 1460446Hom.: 0 Cov.: 30 AF XY: 0.0000110 AC XY: 8AN XY: 726538
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GnomAD4 genome AF: 0.00000657 AC: 1AN: 152136Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 74354
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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 | Mar 11, 2022 | The c.44T>C (p.L15P) alteration is located in exon 1 (coding exon 1) of the OR2J2 gene. This alteration results from a T to C substitution at nucleotide position 44, causing the leucine (L) at amino acid position 15 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
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Uncertain
Eigen
Uncertain
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
.;T
M_CAP
Benign
T
MetaRNN
Uncertain
D;D
MetaSVM
Benign
T
MutationTaster
Benign
D
PrimateAI
Benign
T
PROVEAN
Pathogenic
.;D
REVEL
Benign
Sift
Pathogenic
.;D
Sift4G
Pathogenic
.;D
Vest4
0.76
MutPred
Loss of stability (P = 0.0086);Loss of stability (P = 0.0086);
MVP
0.48
MPC
0.52
ClinPred
D
GERP RS
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