chr22-50221635-C-T
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Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 2P and 13B. PM2BP4_StrongBP6_Very_StrongBP7
The NM_020461.4(TUBGCP6):c.2724G>A(p.Pro908Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000603 in 1,530,104 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.00047 ( 0 hom., cov: 34)
Exomes 𝑓: 0.00062 ( 1 hom. )
Consequence
TUBGCP6
NM_020461.4 synonymous
NM_020461.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.0730
Genes affected
TUBGCP6 (HGNC:18127): (tubulin gamma complex component 6) The protein encoded by this gene is part of a large multisubunit complex required for microtubule nucleation at the centrosome. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.74).
BP6
Variant 22-50221635-C-T is Benign according to our data. Variant chr22-50221635-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 437154.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr22-50221635-C-T is described in Lovd as [Likely_benign].
BP7
Synonymous conserved (PhyloP=-0.073 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TUBGCP6 | NM_020461.4 | c.2724G>A | p.Pro908Pro | synonymous_variant | 16/25 | ENST00000248846.10 | NP_065194.3 | |
TUBGCP6 | XR_001755343.3 | n.3288G>A | non_coding_transcript_exon_variant | 16/20 | ||||
TUBGCP6 | XR_938347.3 | n.3288G>A | non_coding_transcript_exon_variant | 16/23 | ||||
TUBGCP6 | XR_007067982.1 | n.3048+393G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TUBGCP6 | ENST00000248846.10 | c.2724G>A | p.Pro908Pro | synonymous_variant | 16/25 | 1 | NM_020461.4 | ENSP00000248846.5 | ||
TUBGCP6 | ENST00000439308.6 | c.2724G>A | p.Pro908Pro | synonymous_variant | 16/25 | 1 | ENSP00000397387.2 | |||
TUBGCP6 | ENST00000498611.5 | n.3257G>A | non_coding_transcript_exon_variant | 16/23 | 1 | |||||
TUBGCP6 | ENST00000491449.5 | n.1031G>A | non_coding_transcript_exon_variant | 8/16 | 5 |
Frequencies
GnomAD3 genomes AF: 0.000473 AC: 72AN: 152190Hom.: 0 Cov.: 34
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GnomAD3 exomes AF: 0.000351 AC: 65AN: 185348Hom.: 0 AF XY: 0.000419 AC XY: 41AN XY: 97788
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GnomAD4 exome AF: 0.000618 AC: 851AN: 1377796Hom.: 1 Cov.: 36 AF XY: 0.000644 AC XY: 435AN XY: 675698
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GnomAD4 genome AF: 0.000473 AC: 72AN: 152308Hom.: 0 Cov.: 34 AF XY: 0.000537 AC XY: 40AN XY: 74478
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ClinVar
Significance: Likely benign
Submissions summary: Benign:4
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Sep 01, 2023 | TUBGCP6: BP4, BP7 - |
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 31, 2024 | - - |
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Apr 01, 2016 | - - |
TUBGCP6-related disorder Benign:1
Likely benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Nov 07, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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