chr1-247451482-C-G
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001004492.2(OR2B11):c.501G>C(p.Thr167=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0051 in 1,614,154 control chromosomes in the GnomAD database, including 388 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.027 ( 196 hom., cov: 33)
Exomes 𝑓: 0.0029 ( 192 hom. )
Consequence
OR2B11
NM_001004492.2 synonymous
NM_001004492.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -3.93
Genes affected
OR2B11 (HGNC:31249): (olfactory receptor family 2 subfamily B member 11) 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 -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BP6
?
Variant 1-247451482-C-G is Benign according to our data. Variant chr1-247451482-C-G is described in ClinVar as [Benign]. Clinvar id is 775700.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0902 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
OR2B11 | NM_001004492.2 | c.501G>C | p.Thr167= | synonymous_variant | 2/2 | ENST00000641149.2 | |
OR2B11 | NR_169840.1 | n.1155G>C | non_coding_transcript_exon_variant | 5/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OR2B11 | ENST00000641149.2 | c.501G>C | p.Thr167= | synonymous_variant | 2/2 | NM_001004492.2 | P1 | ||
OR2B11 | ENST00000641527.1 | c.501G>C | p.Thr167= | synonymous_variant | 3/3 | P1 | |||
OR2B11 | ENST00000641613.1 | n.1155G>C | non_coding_transcript_exon_variant | 5/5 |
Frequencies
GnomAD3 genomes ? AF: 0.0264 AC: 4023AN: 152182Hom.: 194 Cov.: 33
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GnomAD3 exomes AF: 0.00702 AC: 1763AN: 251176Hom.: 86 AF XY: 0.00509 AC XY: 691AN XY: 135792
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GnomAD4 exome AF: 0.00286 AC: 4186AN: 1461854Hom.: 192 Cov.: 71 AF XY: 0.00247 AC XY: 1798AN XY: 727226
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GnomAD4 genome ? AF: 0.0265 AC: 4041AN: 152300Hom.: 196 Cov.: 33 AF XY: 0.0258 AC XY: 1922AN XY: 74466
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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
Benign, criteria provided, single submitter | clinical testing | Invitae | Jul 31, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
Cadd
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Dann
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at