X-53082576-CCCGCCGCCGCCG-CCCGCCGCCGCCGCCGCCG
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_022117.4(TSPYL2):c.95_100dupCGCCGC(p.Pro32_Pro33dup) variant causes a disruptive inframe insertion change. The variant allele was found at a frequency of 0.00129 in 1,146,877 control chromosomes in the GnomAD database, including 6 homozygotes. There are 304 hemizygotes in GnomAD. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.0017 ( 1 hom., 48 hem., cov: 23)
Exomes 𝑓: 0.0012 ( 5 hom. 256 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 Likely_benign. Variant got -4 ACMG points.
BS2
High Hemizygotes in GnomAd4 at 48 gene
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TSPYL2 | ENST00000375442.8 | c.95_100dupCGCCGC | p.Pro32_Pro33dup | disruptive_inframe_insertion | Exon 1 of 7 | 1 | NM_022117.4 | ENSP00000364591.4 | ||
TSPYL2 | ENST00000579390.1 | c.95_100dupCGCCGC | p.Pro32_Pro33dup | disruptive_inframe_insertion | Exon 1 of 3 | 5 | ENSP00000462287.1 | |||
TSPYL2 | ENST00000553557.5 | n.227_232dupCGCCGC | non_coding_transcript_exon_variant | Exon 1 of 4 | 2 |
Frequencies
GnomAD3 genomes AF: 0.00169 AC: 187AN: 110856Hom.: 1 Cov.: 23 AF XY: 0.00135 AC XY: 45AN XY: 33330
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GnomAD3 exomes AF: 0.00150 AC: 100AN: 66535Hom.: 1 AF XY: 0.000551 AC XY: 12AN XY: 21791
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GnomAD4 exome AF: 0.00125 AC: 1290AN: 1035994Hom.: 5 Cov.: 32 AF XY: 0.000761 AC XY: 256AN XY: 336598
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GnomAD4 genome AF: 0.00171 AC: 190AN: 110883Hom.: 1 Cov.: 23 AF XY: 0.00144 AC XY: 48AN XY: 33369
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ClinVar
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at