chr19-9214484-C-T
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Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001005191.3(OR7D4):c.354G>A(p.Met118Ile) variant causes a missense change. The variant allele was found at a frequency of 0.00000805 in 1,614,012 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.000013 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0000075 ( 0 hom. )
Consequence
OR7D4
NM_001005191.3 missense
NM_001005191.3 missense
Scores
3
7
9
Clinical Significance
Conservation
PhyloP100: 4.81
Genes affected
OR7D4 (HGNC:8380): (olfactory receptor family 7 subfamily D 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]
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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 |
---|---|---|---|---|---|---|---|
OR7D4 | NM_001005191.3 | c.354G>A | p.Met118Ile | missense_variant | 2/2 | ENST00000641669.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OR7D4 | ENST00000641669.1 | c.354G>A | p.Met118Ile | missense_variant | 2/2 | NM_001005191.3 | P1 | ||
OR7D4 | ENST00000308682.3 | c.354G>A | p.Met118Ile | missense_variant | 1/1 | P1 | |||
OR7D4 | ENST00000641244.1 | c.354G>A | p.Met118Ile | missense_variant | 2/2 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152134Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000199 AC: 5AN: 251484Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135918
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GnomAD4 exome AF: 0.00000752 AC: 11AN: 1461878Hom.: 0 Cov.: 34 AF XY: 0.00000963 AC XY: 7AN XY: 727244
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GnomAD4 genome AF: 0.0000131 AC: 2AN: 152134Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74314
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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 01, 2024 | The c.354G>A (p.M118I) alteration is located in exon 1 (coding exon 1) of the OR7D4 gene. This alteration results from a G to A substitution at nucleotide position 354, causing the methionine (M) at amino acid position 118 to be replaced by an isoleucine (I). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Uncertain
DANN
Uncertain
DEOGEN2
Benign
T;T;T
Eigen
Pathogenic
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
.;.;T
M_CAP
Benign
T
MetaRNN
Uncertain
T;T;T
MetaSVM
Benign
T
MutationAssessor
Pathogenic
H;H;H
MutationTaster
Benign
D
PrimateAI
Benign
T
PROVEAN
Uncertain
.;.;D
REVEL
Benign
Sift
Uncertain
.;.;D
Sift4G
Uncertain
.;.;D
Polyphen
D;D;D
Vest4
0.51
MutPred
Loss of methylation at R122 (P = 0.3664);Loss of methylation at R122 (P = 0.3664);Loss of methylation at R122 (P = 0.3664);
MVP
0.72
MPC
0.050
ClinPred
D
GERP RS
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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