chr22-50217753-A-AGTT
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Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PM4_Supporting
The NM_020461.4(TUBGCP6):c.5442_5443insAAC(p.Asn1814dup) variant causes a inframe insertion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000235 in 1,613,844 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.00011 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000015 ( 0 hom. )
Consequence
TUBGCP6
NM_020461.4 inframe_insertion
NM_020461.4 inframe_insertion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 1.94
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 3 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
PM4
Nonframeshift variant in NON repetitive region in NM_020461.4. Strenght limited to Supporting due to length of the change: 1aa.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TUBGCP6 | NM_020461.4 | c.5442_5443insAAC | p.Asn1814dup | inframe_insertion | 25/25 | ENST00000248846.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TUBGCP6 | ENST00000248846.10 | c.5442_5443insAAC | p.Asn1814dup | inframe_insertion | 25/25 | 1 | NM_020461.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000105 AC: 16AN: 151970Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.0000478 AC: 12AN: 251032Hom.: 0 AF XY: 0.0000368 AC XY: 5AN XY: 135764
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GnomAD4 exome AF: 0.0000151 AC: 22AN: 1461756Hom.: 0 Cov.: 34 AF XY: 0.0000138 AC XY: 10AN XY: 727170
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GnomAD4 genome AF: 0.000105 AC: 16AN: 152088Hom.: 0 Cov.: 33 AF XY: 0.000108 AC XY: 8AN XY: 74358
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Aug 08, 2022 | This variant, c.5440_5442dup, results in the insertion of 1 amino acid(s) of the TUBGCP6 protein (p.Asn1814dup), but otherwise preserves the integrity of the reading frame. This variant is present in population databases (rs760483595, gnomAD 0.04%). This variant has not been reported in the literature in individuals affected with TUBGCP6-related conditions. ClinVar contains an entry for this variant (Variation ID: 962289). Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. - |
Computational scores
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at