3-186554367-C-T
Variant names:
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BA1
The NM_018138.5(TBCCD1):c.1431G>A(p.Gly477Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00394 in 1,614,126 control chromosomes in the GnomAD database, including 197 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.020 ( 100 hom., cov: 32)
Exomes 𝑓: 0.0023 ( 97 hom. )
Consequence
TBCCD1
NM_018138.5 synonymous
NM_018138.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.26
Genes affected
TBCCD1 (HGNC:25546): (TBCC domain containing 1) Involved in several processes, including maintenance of Golgi location; maintenance of centrosome location; and regulation of cell shape. Located in spindle pole centrosome. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -19 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.34).
BP6
Variant 3-186554367-C-T is Benign according to our data. Variant chr3-186554367-C-T is described in ClinVar as [Benign]. Clinvar id is 781974.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=1.26 with no splicing effect.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0662 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TBCCD1 | NM_018138.5 | c.1431G>A | p.Gly477Gly | synonymous_variant | Exon 6 of 8 | ENST00000338733.10 | NP_060608.1 | |
TBCCD1 | NM_001134415.1 | c.1431G>A | p.Gly477Gly | synonymous_variant | Exon 6 of 8 | NP_001127887.1 | ||
TBCCD1 | NM_001286749.2 | c.1143G>A | p.Gly381Gly | synonymous_variant | Exon 5 of 7 | NP_001273678.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TBCCD1 | ENST00000338733.10 | c.1431G>A | p.Gly477Gly | synonymous_variant | Exon 6 of 8 | 1 | NM_018138.5 | ENSP00000341652.5 | ||
TBCCD1 | ENST00000424280.5 | c.1431G>A | p.Gly477Gly | synonymous_variant | Exon 6 of 8 | 5 | ENSP00000411253.1 | |||
TBCCD1 | ENST00000446782.5 | c.1143G>A | p.Gly381Gly | synonymous_variant | Exon 5 of 7 | 2 | ENSP00000397091.1 | |||
TBCCD1 | ENST00000479590.1 | n.109G>A | non_coding_transcript_exon_variant | Exon 1 of 2 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0196 AC: 2985AN: 152116Hom.: 97 Cov.: 32
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GnomAD3 exomes AF: 0.00563 AC: 1415AN: 251410Hom.: 40 AF XY: 0.00408 AC XY: 555AN XY: 135894
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GnomAD4 exome AF: 0.00229 AC: 3346AN: 1461892Hom.: 97 Cov.: 32 AF XY: 0.00199 AC XY: 1445AN XY: 727246
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GnomAD4 genome AF: 0.0197 AC: 3006AN: 152234Hom.: 100 Cov.: 32 AF XY: 0.0187 AC XY: 1395AN XY: 74420
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Jul 18, 2018
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
- -
-
Breakthrough Genomics, Breakthrough Genomics
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: not provided
- -
Computational scores
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Name
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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