rs35306023
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Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_ModerateBP6_Very_StrongBP7
The NM_144628.4(TBC1D20):c.1005G>A(p.Gln335=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000342 in 1,614,266 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.0017 ( 1 hom., cov: 33)
Exomes 𝑓: 0.00020 ( 1 hom. )
Consequence
TBC1D20
NM_144628.4 synonymous
NM_144628.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 2.09
Genes affected
TBC1D20 (HGNC:16133): (TBC1 domain family member 20) This gene encodes a protein that belongs to a family of GTPase activator proteins of Rab-like small GTPases. The encoded protein and its cognate GTPase, Rab1, bind the nonstructural protein 5A (NS5A) of the hepatitis C virus (HCV) to mediate viral replication. Depletion of this protein inhibits replication of the virus and HCV infection. Mutations in this gene are associated with Warburg micro syndrome 4. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2014]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.45).
BP6
?
Variant 20-438793-C-T is Benign according to our data. Variant chr20-438793-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 436943.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr20-438793-C-T is described in Lovd as [Likely_benign].
BP7
?
Synonymous conserved (PhyloP=2.09 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TBC1D20 | NM_144628.4 | c.1005G>A | p.Gln335= | synonymous_variant | 8/8 | ENST00000354200.5 | |
TBC1D20 | NR_111901.2 | n.1133G>A | non_coding_transcript_exon_variant | 8/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TBC1D20 | ENST00000354200.5 | c.1005G>A | p.Gln335= | synonymous_variant | 8/8 | 1 | NM_144628.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00175 AC: 266AN: 152258Hom.: 1 Cov.: 33
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GnomAD3 exomes AF: 0.000409 AC: 102AN: 249410Hom.: 0 AF XY: 0.000304 AC XY: 41AN XY: 135000
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GnomAD4 exome AF: 0.000196 AC: 286AN: 1461890Hom.: 1 Cov.: 31 AF XY: 0.000161 AC XY: 117AN XY: 727244
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GnomAD4 genome ? AF: 0.00175 AC: 266AN: 152376Hom.: 1 Cov.: 33 AF XY: 0.00160 AC XY: 119AN XY: 74516
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 10, 2021 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 19, 2024 | - - |
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Jan 08, 2016 | - - |
Computational scores
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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