rs8109935
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001005191.3(OR7D4):c.651C>T(p.Ser217=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0949 in 1,613,186 control chromosomes in the GnomAD database, including 10,447 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.15 ( 2773 hom., cov: 31)
Exomes 𝑓: 0.089 ( 7674 hom. )
Consequence
OR7D4
NM_001005191.3 synonymous
NM_001005191.3 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.246
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 Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.61).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.319 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
OR7D4 | NM_001005191.3 | c.651C>T | p.Ser217= | synonymous_variant | 2/2 | ENST00000641669.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OR7D4 | ENST00000641669.1 | c.651C>T | p.Ser217= | synonymous_variant | 2/2 | NM_001005191.3 | P1 | ||
OR7D4 | ENST00000308682.3 | c.651C>T | p.Ser217= | synonymous_variant | 1/1 | P1 | |||
OR7D4 | ENST00000641244.1 | c.651C>T | p.Ser217= | synonymous_variant | 2/2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.150 AC: 22728AN: 151974Hom.: 2766 Cov.: 31
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GnomAD3 exomes AF: 0.109 AC: 27439AN: 251330Hom.: 2228 AF XY: 0.110 AC XY: 14926AN XY: 135844
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GnomAD4 exome AF: 0.0892 AC: 130318AN: 1461094Hom.: 7674 Cov.: 33 AF XY: 0.0925 AC XY: 67206AN XY: 726884
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GnomAD4 genome ? AF: 0.150 AC: 22763AN: 152092Hom.: 2773 Cov.: 31 AF XY: 0.148 AC XY: 10994AN XY: 74354
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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