Genetic Variant TSPYL2:p.Pro32_Pro33dup (chrX-53082576-C-CCCGCCG) – 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.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

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 48 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.95_100dupCGCCGC	p.Pro32_Pro33dup	disruptive_inframe_insertion	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.95_100dupCGCCGC	p.Pro32_Pro33dup	disruptive_inframe_insertion	Exon 1 of 7	ENSP00000364591.4	Q9H2G4
TSPYL2	ENST00000912653.1		c.95_100dupCGCCGC	p.Pro32_Pro33dup	disruptive_inframe_insertion	Exon 1 of 7	ENSP00000582712.1
TSPYL2	ENST00000887608.1		c.95_100dupCGCCGC	p.Pro32_Pro33dup	disruptive_inframe_insertion	Exon 1 of 7	ENSP00000557667.1

Frequencies

GnomAD3 genomes

AF:

0.00169

AC:

187

AN:

110856

Hom.:

Cov.:

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

GnomAD2 exomes

AF:

0.00150

AC:

100

AN:

66535

AF XY:

0.000551

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 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.:

Cov.:

AF XY:

0.000761

AC XY:

256

AN XY:

336598

show subpopulations

African (AFR)

AF:

0.00189

AC:

AN:

24313

American (AMR)

AF:

0.00332

AC:

AN:

27148

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

18225

East Asian (EAS)

AF:

0.000336

AC:

AN:

26776

South Asian (SAS)

AF:

0.000941

AC:

AN:

48899

European-Finnish (FIN)

AF:

0.000174

AC:

AN:

28704

Middle Eastern (MID)

AF:

0.000655

AC:

AN:

3052

European-Non Finnish (NFE)

AF:

0.00128

AC:

1043

AN:

815083

Other (OTH)

AF:

0.00112

AC:

AN:

43794

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.437

Heterozygous variant carriers

110

164

219

274

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

114

152

190

<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:

0.00171

AC:

190

AN:

110883

Hom.:

Cov.:

AF XY:

0.00144

AC XY:

AN XY:

33369

show subpopulations

African (AFR)

AF:

0.00252

AC:

AN:

30592

American (AMR)

AF:

0.00179

AC:

AN:

10605

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

2637

East Asian (EAS)

AF:

0.00

AC:

AN:

3469

South Asian (SAS)

AF:

0.00370

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:

0.00158

AC:

AN:

52627

Other (OTH)

AF:

0.000661

AC:

AN:

1512

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

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:

0.000585

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

4.3

Mutation Taster

=88/12

polymorphism

(source)

Splicing

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

Publications

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X-53082576-CCCGCCGCCGCCG-CCCGCCGCCGCCGCCGCCG

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