chr17-3062708-C-T
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Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_014566.1(OR1D5):c.900G>A(p.Pro300=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000198 in 1,587,880 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00031 ( 0 hom., cov: 31)
Exomes 𝑓: 0.00019 ( 0 hom. )
Consequence
OR1D5
NM_014566.1 synonymous
NM_014566.1 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.981
Genes affected
OR1D5 (HGNC:8186): (olfactory receptor family 1 subfamily D member 5) 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 Likely_benign. Variant got -5 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BP6
Variant 17-3062708-C-T is Benign according to our data. Variant chr17-3062708-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2647228.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-0.981 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
OR1D5 | NM_014566.1 | c.900G>A | p.Pro300= | synonymous_variant | 1/1 | ENST00000575751.1 | NP_055381.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
OR1D5 | ENST00000575751.1 | c.900G>A | p.Pro300= | synonymous_variant | 1/1 | NM_014566.1 | ENSP00000459028 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000310 AC: 47AN: 151598Hom.: 0 Cov.: 31
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GnomAD3 exomes AF: 0.000103 AC: 25AN: 241566Hom.: 0 AF XY: 0.000122 AC XY: 16AN XY: 131552
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GnomAD4 exome AF: 0.000186 AC: 267AN: 1436166Hom.: 0 Cov.: 29 AF XY: 0.000182 AC XY: 130AN XY: 715842
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GnomAD4 genome AF: 0.000310 AC: 47AN: 151714Hom.: 0 Cov.: 31 AF XY: 0.000270 AC XY: 20AN XY: 74094
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jul 01, 2022 | OR1D5: BP4, BP7 - |
Computational scores
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Benign
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Benign
DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at