chr20-13580985-T-TA
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1
The NM_017714.3(TASP1):c.404-5_404-4insT variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.119 in 1,397,686 control chromosomes in the GnomAD database, including 115 homozygotes. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0066 ( 8 hom., cov: 0)
Exomes 𝑓: 0.13 ( 107 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: 3.41
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 Benign. Variant got -10 ACMG points.
BP6
?
Variant 20-13580985-T-TA is Benign according to our data. Variant chr20-13580985-T-TA is described in ClinVar as [Benign]. Clinvar id is 3059573.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAdExome4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.139 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TASP1 | NM_017714.3 | c.404-5_404-4insT | 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.404-5_404-4insT | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_017714.3 | P1 | |||
TASP1 | ENST00000455532.5 | c.335-5_335-4insT | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 5 | |||||
TASP1 | ENST00000465381.5 | n.488-5_488-4insT | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant | 5 | |||||
TASP1 | ENST00000480436.5 | n.488-5_488-4insT | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00656 AC: 917AN: 139846Hom.: 7 Cov.: 0
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GnomAD4 exome AF: 0.131 AC: 165342AN: 1257798Hom.: 107 Cov.: 21 AF XY: 0.132 AC XY: 83009AN XY: 626928
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GnomAD4 genome ? AF: 0.00663 AC: 927AN: 139888Hom.: 8 Cov.: 0 AF XY: 0.00816 AC XY: 552AN XY: 67652
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
TASP1-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jan 14, 2020 | This variant is classified as 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