8-102275711-T-A
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Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7
The NM_015902.6(UBR5):c.6627A>T(p.Gly2209=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000205 in 1,461,778 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: not found (cov: 32)
Exomes 𝑓: 0.0000021 ( 0 hom. )
Consequence
UBR5
NM_015902.6 synonymous
NM_015902.6 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 2.00
Genes affected
UBR5 (HGNC:16806): (ubiquitin protein ligase E3 component n-recognin 5) This gene encodes a progestin-induced protein, which belongs to the HECT (homology to E6-AP carboxyl terminus) family. The HECT family proteins function as E3 ubiquitin-protein ligases, targeting specific proteins for ubiquitin-mediated proteolysis. This gene is localized to chromosome 8q22 which is disrupted in a variety of cancers. This gene potentially has a role in regulation of cell proliferation or differentiation. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -3 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.35).
BP6
Variant 8-102275711-T-A is Benign according to our data. Variant chr8-102275711-T-A is described in ClinVar as [Likely_benign]. Clinvar id is 2658723.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=2.01 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
UBR5 | NM_015902.6 | c.6627A>T | p.Gly2209= | synonymous_variant | 46/59 | ENST00000520539.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
UBR5 | ENST00000520539.6 | c.6627A>T | p.Gly2209= | synonymous_variant | 46/59 | 1 | NM_015902.6 | P5 | |
UBR5 | ENST00000220959.8 | c.6627A>T | p.Gly2209= | synonymous_variant | 46/59 | 1 | A1 | ||
UBR5 | ENST00000521922.5 | c.6609A>T | p.Gly2203= | synonymous_variant | 46/59 | 5 | A1 | ||
UBR5 | ENST00000521566.1 | c.102A>T | p.Gly34= | synonymous_variant | 2/5 | 4 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
Cov.:
32
GnomAD4 exome AF: 0.00000205 AC: 3AN: 1461778Hom.: 0 Cov.: 35 AF XY: 0.00000413 AC XY: 3AN XY: 727180
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GnomAD4 genome Cov.: 32
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32
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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 | Oct 01, 2022 | UBR5: PM2:Supporting, BP4, BP7 - |
Computational scores
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Name
Calibrated prediction
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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