Genetic Variant NM_022117.4:c.95_100delCGCCGC (chrX-53082576-CCCGCCG-C) – ACMG Classification: Likely_benign (-6 pts)

Variant summary

Our verdict is Likely benign. The variant received -6 ACMG points: 0P and 6B. BP6_ModerateBS2

The NM_022117.4(TSPYL2):c.95_100delCGCCGC(p.Pro32_Pro33del) variant causes a disruptive inframe deletion change. The variant allele was found at a frequency of 0.000894 in 1,146,989 control chromosomes in the GnomAD database, including 1 homozygotes. There are 284 hemizygotes in GnomAD. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.00074 ( 1 hom., 22 hem., cov: 23)

Exomes 𝑓: 0.00091 ( 0 hom. 262 hem. )

Consequence

TSPYL2
NM_022117.4 disruptive_inframe_deletion

Scores

Not classified

Clinical Significance

Likely benign criteria provided, single submitter B:1

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 -6 ACMG points.

BP6

Variant X-53082576-CCCGCCG-C is Benign according to our data. Variant chrX-53082576-CCCGCCG-C is described in ClinVar as Likely_benign. ClinVar VariationId is 810606.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Hemizygotes in GnomAd4 at 22 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_100delCGCCGC	p.Pro32_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.95_100delCGCCGC	p.Pro32_Pro33del	disruptive_inframe_deletion	Exon 1 of 7	ENSP00000364591.4	Q9H2G4
TSPYL2	ENST00000912653.1		c.95_100delCGCCGC	p.Pro32_Pro33del	disruptive_inframe_deletion	Exon 1 of 7	ENSP00000582712.1
TSPYL2	ENST00000887608.1		c.95_100delCGCCGC	p.Pro32_Pro33del	disruptive_inframe_deletion	Exon 1 of 7	ENSP00000557667.1

Frequencies

GnomAD3 genomes

AF:

0.000740

AC:

AN:

110857

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000557

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000378

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.000574

Gnomad SAS

AF:

0.00147

Gnomad FIN

AF:

0.000171

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000988

Gnomad OTH

AF:

0.00134

GnomAD2 exomes

AF:

0.000872

AC:

AN:

66535

AF XY:

0.000505

show subpopulations

Gnomad AFR exome

AF:

0.000376

Gnomad AMR exome

AF:

0.000634

Gnomad ASJ exome

AF:

0.000459

Gnomad EAS exome

AF:

0.00101

Gnomad FIN exome

AF:

0.00209

Gnomad NFE exome

AF:

0.00113

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.000910

AC:

943

AN:

1036105

Hom.:

AF XY:

0.000778

AC XY:

262

AN XY:

336727

show subpopulations

African (AFR)

AF:

0.000288

AC:

AN:

24310

American (AMR)

AF:

0.000405

AC:

AN:

27163

Ashkenazi Jewish (ASJ)

AF:

0.000110

AC:

AN:

18224

East Asian (EAS)

AF:

0.000598

AC:

AN:

26764

South Asian (SAS)

AF:

0.000572

AC:

AN:

48914

European-Finnish (FIN)

AF:

0.00129

AC:

AN:

28698

Middle Eastern (MID)

AF:

0.000983

AC:

AN:

3051

European-Non Finnish (NFE)

AF:

0.000980

AC:

799

AN:

815174

Other (OTH)

AF:

0.000913

AC:

AN:

43807

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.479

Heterozygous variant carriers

133

178

222

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

102

136

170

<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:

0.000740

AC:

AN:

110884

Hom.:

Cov.:

AF XY:

0.000659

AC XY:

AN XY:

33372

show subpopulations

African (AFR)

AF:

0.000556

AC:

AN:

30590

American (AMR)

AF:

0.000377

AC:

AN:

10605

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

2637

East Asian (EAS)

AF:

0.000577

AC:

AN:

3469

South Asian (SAS)

AF:

0.00148

AC:

AN:

2704

European-Finnish (FIN)

AF:

0.000171

AC:

AN:

5857

Middle Eastern (MID)

AF:

0.00

AC:

AN:

209

European-Non Finnish (NFE)

AF:

0.000988

AC:

AN:

52630

Other (OTH)

AF:

0.00132

AC:

AN:

1512

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.495

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:

0.000292

Hom.:

Bravo

AF:

0.000631

ClinVar

ClinVar submissions

Significance:Likely benign

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

4.3

Mutation Taster

=198/2

polymorphism

(source)

Splicing

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

Publications

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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