Genetic Variant TSPYL2:p.Pro31_Pro33del (chrX-53082576-CCCGCCGCCG-C) – ACMG Classification: Likely_benign (-4 pts)

Variant summary

Our verdict is Likely benign. The variant received -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

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 4.25

Publications

2 publications found

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]

TSPYL2 links:

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -4 ACMG points.

BS2

High Hemizygotes in GnomAd4 at 26 gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_022117.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TSPYL2	NM_022117.4	MANE Select	c.92_100delCGCCGCCGC	p.Pro31_Pro33del	disruptive_inframe_deletion	Exon 1 of 7	NP_071400.1	Q9H2G4

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
TSPYL2	ENST00000375442.8	TSL:1 MANE Select	c.92_100delCGCCGCCGC	p.Pro31_Pro33del	disruptive_inframe_deletion	Exon 1 of 7	ENSP00000364591.4	Q9H2G4
TSPYL2	ENST00000912653.1		c.92_100delCGCCGCCGC	p.Pro31_Pro33del	disruptive_inframe_deletion	Exon 1 of 7	ENSP00000582712.1
TSPYL2	ENST00000887608.1		c.92_100delCGCCGCCGC	p.Pro31_Pro33del	disruptive_inframe_deletion	Exon 1 of 7	ENSP00000557667.1

Frequencies

GnomAD3 genomes

AF:

0.000695

AC:

AN:

110858

Hom.:

Cov.:

show subpopulations

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

GnomAD2 exomes

AF:

0.00168

AC:

112

AN:

66535

AF XY:

0.00174

show subpopulations

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 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.:

AF XY:

0.000517

AC XY:

174

AN XY:

336798

show subpopulations

African (AFR)

AF:

0.00144

AC:

AN:

24325

American (AMR)

AF:

0.000368

AC:

AN:

27174

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

18226

East Asian (EAS)

AF:

0.0138

AC:

370

AN:

26775

South Asian (SAS)

AF:

0.000123

AC:

AN:

48926

European-Finnish (FIN)

AF:

0.0000348

AC:

AN:

28703

Middle Eastern (MID)

AF:

0.000983

AC:

AN:

3052

European-Non Finnish (NFE)

AF:

0.000173

AC:

141

AN:

815230

Other (OTH)

AF:

0.000593

AC:

AN:

43813

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

118

148

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

100

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.000685

AC:

AN:

110885

Hom.:

Cov.:

AF XY:

0.000779

AC XY:

AN XY:

33371

show subpopulations

African (AFR)

AF:

0.000817

AC:

AN:

30592

American (AMR)

AF:

0.000377

AC:

AN:

10605

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

2637

East Asian (EAS)

AF:

0.0115

AC:

AN:

3469

South Asian (SAS)

AF:

0.000370

AC:

AN:

2704

European-Finnish (FIN)

AF:

0.00

AC:

AN:

5857

Middle Eastern (MID)

AF:

0.00

AC:

AN:

209

European-Non Finnish (NFE)

AF:

0.0000760

AC:

AN:

52630

Other (OTH)

AF:

0.00132

AC:

AN:

1511

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.462

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.000329

Hom.:

Bravo

AF:

0.000994

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

4.3

Mutation Taster

=195/5

polymorphism (auto)

(source)

Splicing

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

Publications

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X-53082576-CCCGCCGCCGCCG-CCCG

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over