chr21-44499743-CCCACCTGGCCACCCCAGTTGCTGCCGGGCAGCCGCGGCCTCAGCGTGTCCTCAG-C
Variant summary
Our verdict is Pathogenic. Variant got 10 ACMG points: 10P and 0B. PVS1PM2
The NM_144991.3(TSPEAR):c.1996_*39delCTGAGGACACGCTGAGGCCGCGGCTGCCCGGCAGCAACTGGGGTGGCCAGGTGG(p.Leu666_Ter670del) variant causes a stop lost, conservative inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000291 in 1,374,138 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_144991.3 stop_lost, conservative_inframe_deletion
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TSPEAR | NM_144991.3 | c.1996_*39delCTGAGGACACGCTGAGGCCGCGGCTGCCCGGCAGCAACTGGGGTGGCCAGGTGG | p.Leu666_Ter670del | stop_lost, conservative_inframe_deletion | 12/12 | ENST00000323084.9 | NP_659428.2 | |
TSPEAR | NM_144991.3 | c.1995_*39delCTGAGGACACGCTGAGGCCGCGGCTGCCCGGCAGCAACTGGGGTGGCCAGGTGG | 3_prime_UTR_variant | 12/12 | ENST00000323084.9 | NP_659428.2 | ||
TSPEAR | NM_001272037.2 | c.1792_*39delCTGAGGACACGCTGAGGCCGCGGCTGCCCGGCAGCAACTGGGGTGGCCAGGTGG | p.Leu598_Ter602del | stop_lost, conservative_inframe_deletion | 13/13 | NP_001258966.1 | ||
TSPEAR | NM_001272037.2 | c.1791_*39delCTGAGGACACGCTGAGGCCGCGGCTGCCCGGCAGCAACTGGGGTGGCCAGGTGG | 3_prime_UTR_variant | 13/13 | NP_001258966.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TSPEAR | ENST00000323084.9 | c.1996_*39delCTGAGGACACGCTGAGGCCGCGGCTGCCCGGCAGCAACTGGGGTGGCCAGGTGG | p.Leu666_Ter670del | stop_lost, conservative_inframe_deletion | 12/12 | 1 | NM_144991.3 | ENSP00000321987.4 | ||
TSPEAR | ENST00000323084 | c.1995_*39delCTGAGGACACGCTGAGGCCGCGGCTGCCCGGCAGCAACTGGGGTGGCCAGGTGG | 3_prime_UTR_variant | 12/12 | 1 | NM_144991.3 | ENSP00000321987.4 | |||
TSPEAR | ENST00000642437.1 | n.*1941_*1994delCTGAGGACACGCTGAGGCCGCGGCTGCCCGGCAGCAACTGGGGTGGCCAGGTGG | non_coding_transcript_exon_variant | 13/13 | ENSP00000496535.1 | |||||
TSPEAR | ENST00000642437.1 | n.*1941_*1994delCTGAGGACACGCTGAGGCCGCGGCTGCCCGGCAGCAACTGGGGTGGCCAGGTGG | 3_prime_UTR_variant | 13/13 | ENSP00000496535.1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome AF: 0.00000291 AC: 4AN: 1374138Hom.: 0 AF XY: 0.00000295 AC XY: 2AN XY: 676940
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | May 02, 2024 | Frameshift variant predicted to result in abnormal protein length as the last 4 amino acids are replaced with 50 different amino acids; Not observed at significant frequency in large population cohorts (gnomAD); Has not been previously published as pathogenic or benign to our knowledge - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.