17-3197642-AATCTGCTCATC-A
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBS1BS2
The NM_012352.3(OR1A2):c.129_139delGCTCATCATCT(p.Leu44GlyfsTer5) variant causes a frameshift change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00148 in 1,608,252 control chromosomes in the GnomAD database, including 32 homozygotes. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0076 ( 15 hom., cov: 32)
Exomes 𝑓: 0.00084 ( 17 hom. )
Consequence
OR1A2
NM_012352.3 frameshift
NM_012352.3 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 8.62
Genes affected
OR1A2 (HGNC:8180): (olfactory receptor family 1 subfamily A 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 Benign. Variant got -10 ACMG points.
BP6
Variant 17-3197642-AATCTGCTCATC-A is Benign according to our data. Variant chr17-3197642-AATCTGCTCATC-A is described in ClinVar as [Benign]. Clinvar id is 777087.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00763 (1162/152212) while in subpopulation AFR AF= 0.0268 (1111/41530). AF 95% confidence interval is 0.0254. There are 15 homozygotes in gnomad4. There are 519 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 15 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
OR1A2 | NM_012352.3 | c.129_139delGCTCATCATCT | p.Leu44GlyfsTer5 | frameshift_variant | Exon 1 of 1 | ENST00000381951.1 | NP_036484.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00761 AC: 1158AN: 152094Hom.: 15 Cov.: 32
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GnomAD3 exomes AF: 0.00203 AC: 494AN: 243578Hom.: 6 AF XY: 0.00141 AC XY: 185AN XY: 131546
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GnomAD4 exome AF: 0.000837 AC: 1219AN: 1456040Hom.: 17 AF XY: 0.000703 AC XY: 509AN XY: 724188
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GnomAD4 genome AF: 0.00763 AC: 1162AN: 152212Hom.: 15 Cov.: 32 AF XY: 0.00697 AC XY: 519AN XY: 74424
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Dec 31, 2019
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
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Computational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at