X-53082576-CCCGCCGCCGCCG-CCCGCCGCCGCCGCCGCCGCCGCCG

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

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 4.25
Variant links:
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

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
TSPYL2NM_022117.4 linkc.89_100dupCGCCGCCGCCGC p.Pro30_Pro33dup disruptive_inframe_insertion Exon 1 of 7 ENST00000375442.8 NP_071400.1 Q9H2G4

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
TSPYL2ENST00000375442.8 linkc.89_100dupCGCCGCCGCCGC p.Pro30_Pro33dup disruptive_inframe_insertion Exon 1 of 7 1 NM_022117.4 ENSP00000364591.4 Q9H2G4
TSPYL2ENST00000579390.1 linkc.89_100dupCGCCGCCGCCGC p.Pro30_Pro33dup disruptive_inframe_insertion Exon 1 of 3 5 ENSP00000462287.1 J3KS33
TSPYL2ENST00000553557.5 linkn.221_232dupCGCCGCCGCCGC non_coding_transcript_exon_variant Exon 1 of 4 2

Frequencies

GnomAD3 genomes
AF:
0.0000180
AC:
2
AN:
110859
Hom.:
0
Cov.:
23
AF XY:
0.00
AC XY:
0
AN XY:
33333
show subpopulations
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000380
Gnomad OTH
AF:
0.00
GnomAD4 exome
AF:
0.00000290
AC:
3
AN:
1036247
Hom.:
0
Cov.:
32
AF XY:
0.00
AC XY:
0
AN XY:
336819
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000368
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
AF:
0.0000180
AC:
2
AN:
110859
Hom.:
0
Cov.:
23
AF XY:
0.00
AC XY:
0
AN XY:
33333
show subpopulations
Gnomad4 AFR
AF:
0.00
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000380
Gnomad4 OTH
AF:
0.00
Bravo
AF:
0.00000756

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs781884842; hg19: chrX-53111758; API