rs404240
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_006398.4(UBD):āc.198T>Cā(p.Tyr66=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0888 in 1,613,028 control chromosomes in the GnomAD database, including 8,318 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: š 0.053 ( 363 hom., cov: 32)
Exomes š: 0.092 ( 7955 hom. )
Consequence
UBD
NM_006398.4 synonymous
NM_006398.4 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.00
Genes affected
UBD (HGNC:18795): (ubiquitin D) This gene encodes a protein which contains two ubiquitin-like domains and appears to have similar function to ubiquitin. Through covalent attachment, the encoded protein targets other proteins for 26S proteasome degradation. This protein has been implicated to function in many cellular processes, including caspase-dependent apoptosis, formation of aggresomes, mitotic regulation, and dendritic cell maturation. Upregulation of this gene may promote inflammation in chronic kidney disease and has been observed in many cancer types. [provided by RefSeq, Aug 2017]
OR2I1P (HGNC:8258): (olfactory receptor family 2 subfamily I member 1 pseudogene) 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]
GABBR1 (HGNC:4070): (gamma-aminobutyric acid type B receptor subunit 1) This gene encodes a receptor for gamma-aminobutyric acid (GABA), which is the main inhibitory neurotransmitter in the mammalian central nervous system. This receptor functions as a heterodimer with GABA(B) receptor 2. Defects in this gene may underlie brain disorders such as schizophrenia and epilepsy. Alternative splicing generates multiple transcript variants, but the full-length nature of some of these variants has not been determined. [provided by RefSeq, Jan 2016]
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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=-0.79).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0925 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
UBD | NM_006398.4 | c.198T>C | p.Tyr66= | synonymous_variant | 2/2 | ENST00000377050.5 | |
OR2I1P | NM_001396058.1 | c.*2014A>G | 3_prime_UTR_variant | 2/2 | ENST00000641137.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
UBD | ENST00000377050.5 | c.198T>C | p.Tyr66= | synonymous_variant | 2/2 | 1 | NM_006398.4 | P1 | |
OR2I1P | ENST00000641137.2 | c.*2014A>G | 3_prime_UTR_variant | 2/2 | NM_001396058.1 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0533 AC: 8113AN: 152160Hom.: 363 Cov.: 32
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GnomAD3 exomes AF: 0.0494 AC: 12192AN: 246602Hom.: 530 AF XY: 0.0495 AC XY: 6647AN XY: 134390
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GnomAD4 exome AF: 0.0925 AC: 135090AN: 1460750Hom.: 7955 Cov.: 37 AF XY: 0.0891 AC XY: 64747AN XY: 726686
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GnomAD4 genome AF: 0.0533 AC: 8109AN: 152278Hom.: 363 Cov.: 32 AF XY: 0.0473 AC XY: 3521AN XY: 74450
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Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
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Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at