chrX-53082576-C-CCCGCCGCCGCCG
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_022117.4(TSPYL2):c.89_100dupCGCCGCCGCCGC(p.Pro30_Pro33dup) variant causes a disruptive inframe insertion change. The variant allele was found at a frequency of 0.00000436 in 1,147,106 control chromosomes in the GnomAD database, with no homozygous occurrence. There are no hemizygote samples in GnomAD. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.000018 ( 0 hom., 0 hem., cov: 23)
Exomes 𝑓: 0.0000029 ( 0 hom. 0 hem. )
Consequence
TSPYL2
NM_022117.4 disruptive_inframe_insertion
NM_022117.4 disruptive_inframe_insertion
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 4.25
Genes affected
TSPYL2 (HGNC:24358): (TSPY like 2) This gene encodes a member of the testis-specific protein Y-encoded, TSPY-like/SET/nucleosome assembly protein-1 superfamily. The encoded protein is localized to the nucleolus where it functions in chromatin remodeling and as an inhibitor of cell-cycle progression. This protein may play a role in the suppression of tumor growth. [provided by RefSeq, Sep 2009]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TSPYL2 | ENST00000375442.8 | c.89_100dupCGCCGCCGCCGC | p.Pro30_Pro33dup | disruptive_inframe_insertion | Exon 1 of 7 | 1 | NM_022117.4 | ENSP00000364591.4 | ||
TSPYL2 | ENST00000579390.1 | c.89_100dupCGCCGCCGCCGC | p.Pro30_Pro33dup | disruptive_inframe_insertion | Exon 1 of 3 | 5 | ENSP00000462287.1 | |||
TSPYL2 | ENST00000553557.5 | n.221_232dupCGCCGCCGCCGC | non_coding_transcript_exon_variant | Exon 1 of 4 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000180 AC: 2AN: 110859Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 33333
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GnomAD4 exome AF: 0.00000290 AC: 3AN: 1036247Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 336819
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GnomAD4 genome AF: 0.0000180 AC: 2AN: 110859Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 33333
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ClinVar
Not reported inComputational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at