chr20-13580985-TAA-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP6_Moderate
The NM_017714.3(TASP1):c.404-6_404-5del variant causes a splice region, splice polypyrimidine tract, intron change. The variant allele was found at a frequency of 0.00118 in 1,458,822 control chromosomes in the GnomAD database, with no homozygous occurrence. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000029 ( 0 hom., cov: 0)
Exomes 𝑓: 0.0013 ( 0 hom. )
Consequence
TASP1
NM_017714.3 splice_region, splice_polypyrimidine_tract, intron
NM_017714.3 splice_region, splice_polypyrimidine_tract, intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 4.00
Genes affected
TASP1 (HGNC:15859): (taspase 1) This gene encodes an endopeptidase that cleaves specific substrates following aspartate residues. The encoded protein undergoes posttranslational autoproteolytic processing to generate alpha and beta subunits, which reassemble into the active alpha2-beta2 heterotetramer. It is required to cleave MLL, a protein required for the maintenance of HOX gene expression, and TFIIA, a basal transcription factor. Alternatively spliced transcript variants have been described, but their biological validity has not been determined. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 0 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP6
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Variant 20-13580985-TAA-T is Benign according to our data. Variant chr20-13580985-TAA-T is described in ClinVar as [Likely_benign]. Clinvar id is 3042908.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TASP1 | NM_017714.3 | c.404-6_404-5del | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000337743.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TASP1 | ENST00000337743.9 | c.404-6_404-5del | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_017714.3 | P1 | |||
TASP1 | ENST00000455532.5 | c.335-6_335-5del | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 5 | |||||
TASP1 | ENST00000465381.5 | n.488-6_488-5del | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant | 5 | |||||
TASP1 | ENST00000480436.5 | n.488-6_488-5del | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000286 AC: 4AN: 139906Hom.: 0 Cov.: 0
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GnomAD4 exome AF: 0.00130 AC: 1715AN: 1318916Hom.: 0 AF XY: 0.00128 AC XY: 838AN XY: 657074
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
TASP1-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Nov 06, 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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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at