X-53082576-CCCGCCGCCGCCG-CCCG

Variant names:

• chrX-53082576-CCCGCCGCCG-C
• rs781884842
• NM_022117.4:c.92_100delCGCCGCCGC

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2

The NM_022117.4(TSPYL2):​c.92_100delCGCCGCCGC​(p.Pro31_Pro33del) variant causes a disruptive inframe deletion change. The variant allele was found at a frequency of 0.000582 in 1,147,109 control chromosomes in the GnomAD database, including 4 homozygotes. There are 200 hemizygotes in GnomAD. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.00069 (0 hom., 26 hem., cov: 23)
  • Exomes 𝑓: 0.00057 (4 hom. 174 hem.)
• Consequence: TSPYL2 NM_022117.4 disruptive_inframe_deletion
• 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]

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BS2: High Hemizygotes in GnomAd4 at 26 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TSPYL2	NM_022117.4	c.92_100delCGCCGCCGC	p.Pro31_Pro33del	disruptive_inframe_deletion	Exon 1 of 7	ENST00000375442.8	NP_071400.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TSPYL2	ENST00000375442.8	c.92_100delCGCCGCCGC	p.Pro31_Pro33del	disruptive_inframe_deletion	Exon 1 of 7	1	NM_022117.4	ENSP00000364591.4
TSPYL2	ENST00000579390.1	c.92_100delCGCCGCCGC	p.Pro31_Pro33del	disruptive_inframe_deletion	Exon 1 of 3	5		ENSP00000462287.1
TSPYL2	ENST00000553557.5	n.224_232delCGCCGCCGC		non_coding_transcript_exon_variant	Exon 1 of 4	2

Frequencies

GnomAD3 genomes AF: 0.000695 AC: 77 AN: 110858 Hom.: 0 Cov.: 23 AF XY: 0.000750 AC XY: 25 AN XY: 33332

Gnomad AFR AF: 0.000819

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000378

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.0118

Gnomad SAS AF: 0.000368

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000760

Gnomad OTH AF: 0.00134

GnomAD3 exomes AF: 0.00168 AC: 112 AN: 66535 Hom.: 2 AF XY: 0.00174 AC XY: 38 AN XY: 21791

Gnomad AFR exome AF: 0.00188

Gnomad AMR exome AF: 0.000211

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.0183

Gnomad SAS exome AF: 0.000298

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.000335

Gnomad OTH exome AF: 0.000959

GnomAD4 exome AF: 0.000571 AC: 592 AN: 1036224 Hom.: 4 AF XY: 0.000517 AC XY: 174 AN XY: 336798

Gnomad4 AFR exome AF: 0.00144

Gnomad4 AMR exome AF: 0.000368

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.0138

Gnomad4 SAS exome AF: 0.000123

Gnomad4 FIN exome AF: 0.0000348

Gnomad4 NFE exome AF: 0.000173

Gnomad4 OTH exome AF: 0.000593

GnomAD4 genome AF: 0.000685 AC: 76 AN: 110885 Hom.: 0 Cov.: 23 AF XY: 0.000779 AC XY: 26 AN XY: 33371

Gnomad4 AFR AF: 0.000817

Gnomad4 AMR AF: 0.000377

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.0115

Gnomad4 SAS AF: 0.000370

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000760

Gnomad4 OTH AF: 0.00132

Bravo AF: 0.000994

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs781884842; hg19: chrX-53111758;