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

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]

Genome browser will be placed here

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

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
TSPYL2NM_022117.4 linkc.95_100dupCGCCGC p.Pro32_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.95_100dupCGCCGC p.Pro32_Pro33dup disruptive_inframe_insertion Exon 1 of 7 1 NM_022117.4 ENSP00000364591.4 Q9H2G4
TSPYL2ENST00000579390.1 linkc.95_100dupCGCCGC p.Pro32_Pro33dup disruptive_inframe_insertion Exon 1 of 3 5 ENSP00000462287.1 J3KS33
TSPYL2ENST00000553557.5 linkn.227_232dupCGCCGC non_coding_transcript_exon_variant Exon 1 of 4 2

Frequencies

GnomAD3 genomes
AF:
0.00169
AC:
187
AN:
110856
Hom.:
1
Cov.:
23
AF XY:
0.00135
AC XY:
45
AN XY:
33330
show subpopulations
Gnomad AFR
AF:
0.00242
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00179
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00368
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00158
Gnomad OTH
AF:
0.000670
GnomAD3 exomes
AF:
0.00150
AC:
100
AN:
66535
Hom.:
1
AF XY:
0.000551
AC XY:
12
AN XY:
21791
show subpopulations
Gnomad AFR exome
AF:
0.00225
Gnomad AMR exome
AF:
0.00317
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.000604
Gnomad SAS exome
AF:
0.000398
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00163
Gnomad OTH exome
AF:
0.00144
GnomAD4 exome
AF:
0.00125
AC:
1290
AN:
1035994
Hom.:
5
Cov.:
32
AF XY:
0.000761
AC XY:
256
AN XY:
336598
show subpopulations
Gnomad4 AFR exome
AF:
0.00189
Gnomad4 AMR exome
AF:
0.00332
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.000336
Gnomad4 SAS exome
AF:
0.000941
Gnomad4 FIN exome
AF:
0.000174
Gnomad4 NFE exome
AF:
0.00128
Gnomad4 OTH exome
AF:
0.00112
GnomAD4 genome
AF:
0.00171
AC:
190
AN:
110883
Hom.:
1
Cov.:
23
AF XY:
0.00144
AC XY:
48
AN XY:
33369
show subpopulations
Gnomad4 AFR
AF:
0.00252
Gnomad4 AMR
AF:
0.00179
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00370
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00158
Gnomad4 OTH
AF:
0.000661

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