rs387907019
Positions:
Variant summary
Our verdict is Uncertain significance. Variant got 5 ACMG points: 5P and 0B. PM2PM4PP5
The NM_020461.4(TUBGCP6):āc.5458T>Gā(p.Ter1820GlyextTer?) variant causes a stop lost change. The variant allele was found at a frequency of 0.00000186 in 1,613,710 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 Pathogenic (no stars).
Frequency
Genomes: š 0.000013 ( 0 hom., cov: 33)
Exomes š: 6.8e-7 ( 0 hom. )
Consequence
TUBGCP6
NM_020461.4 stop_lost
NM_020461.4 stop_lost
Scores
1
2
4
Clinical Significance
Conservation
PhyloP100: 5.81
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 5 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
PM4
?
Stoplost variant in NM_020461.4 Downstream stopcodon found after 1 codons.
PP5
?
Variant 22-50217738-A-C is Pathogenic according to our data. Variant chr22-50217738-A-C is described in ClinVar as [Pathogenic]. Clinvar id is 30809.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr22-50217738-A-C is described in Lovd as [Likely_pathogenic].
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TUBGCP6 | NM_020461.4 | c.5458T>G | p.Ter1820GlyextTer? | stop_lost | 25/25 | ENST00000248846.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TUBGCP6 | ENST00000248846.10 | c.5458T>G | p.Ter1820GlyextTer? | stop_lost | 25/25 | 1 | NM_020461.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152160Hom.: 0 Cov.: 33
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GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461550Hom.: 0 Cov.: 34 AF XY: 0.00000138 AC XY: 1AN XY: 727074
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GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152160Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74334
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ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Microcephaly and chorioretinopathy 1 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Jan 01, 2012 | - - |
Computational scores
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Name
Calibrated prediction
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Prediction
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
MutationTaster
Benign
D;N
Vest4
GERP RS
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