X-53082576-CCCGCCGCCGCCG-CCCGCCGCCG

Variant names:

• chrX-53082576-CCCG-C
• rs781884842
• NM_022117.4:c.98_100delCGC

Variant summary

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

The NM_022117.4(TSPYL2):​c.98_100delCGC​(p.Pro33del) variant causes a disruptive inframe deletion change. The variant allele was found at a frequency of 0.000475 in 1,100,532 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 6 hemizygotes in GnomAD. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.000045 (0 hom., 1 hem., cov: 23)
  • Exomes 𝑓: 0.00052 (0 hom. 5 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 GnomAdExome4 at 5 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TSPYL2	NM_022117.4	c.98_100delCGC	p.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.98_100delCGC	p.Pro33del	disruptive_inframe_deletion	Exon 1 of 7	1	NM_022117.4	ENSP00000364591.4
TSPYL2	ENST00000579390.1	c.98_100delCGC	p.Pro33del	disruptive_inframe_deletion	Exon 1 of 3	5		ENSP00000462287.1
TSPYL2	ENST00000553557.5	n.230_232delCGC		non_coding_transcript_exon_variant	Exon 1 of 4	2

Frequencies

GnomAD3 genomes AF: 0.0000451 AC: 5 AN: 110819 Hom.: 0 Cov.: 23 AF XY: 0.0000300 AC XY: 1 AN XY: 33317

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0000945

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.000171

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000570

Gnomad OTH AF: 0.00

GnomAD3 exomes AF: 0.00651 AC: 433 AN: 66535 Hom.: 0 AF XY: 0.000138 AC XY: 3 AN XY: 21791

Gnomad AFR exome AF: 0.0222

Gnomad AMR exome AF: 0.00472

Gnomad ASJ exome AF: 0.00803

Gnomad EAS exome AF: 0.00805

Gnomad SAS exome AF: 0.00269

Gnomad FIN exome AF: 0.00951

Gnomad NFE exome AF: 0.00615

Gnomad OTH exome AF: 0.00815

GnomAD4 exome AF: 0.000523 AC: 518 AN: 989691 Hom.: 0 AF XY: 0.0000158 AC XY: 5 AN XY: 315893

Gnomad4 AFR exome AF: 0.00286

Gnomad4 AMR exome AF: 0.00314

Gnomad4 ASJ exome AF: 0.00183

Gnomad4 EAS exome AF: 0.00143

Gnomad4 SAS exome AF: 0.000529

Gnomad4 FIN exome AF: 0.00157

Gnomad4 NFE exome AF: 0.000272

Gnomad4 OTH exome AF: 0.000626

GnomAD4 genome AF: 0.0000451 AC: 5 AN: 110841 Hom.: 0 Cov.: 23 AF XY: 0.0000300 AC XY: 1 AN XY: 33351

Gnomad4 AFR AF: 0.00

Gnomad4 AMR AF: 0.0000944

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.000171

Gnomad4 NFE AF: 0.0000570

Gnomad4 OTH AF: 0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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;