Variant X-53084628-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2

The NM_022117.4(TSPYL2):c.885+6G>A variant causes a splice donor region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00888 in 1,204,804 control chromosomes in the GnomAD database, including 41 homozygotes. There are 3,362 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0059 ( 1 hom., 152 hem., cov: 22)

Exomes 𝑓: 0.0092 ( 40 hom. 3210 hem. )

Consequence

TSPYL2
NM_022117.4 splice_donor_region, intron

Scores

Splicing: ADA: 0.00003185

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.618

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 made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.59).

BP6

Variant X-53084628-G-A is Benign according to our data. Variant chrX-53084628-G-A is described in ClinVar as [Benign]. Clinvar id is 788495.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-53084628-G-A is described in Lovd as [Likely_benign].

BS2

High Hemizygotes in GnomAd4 at 152 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TSPYL2	NM_022117.4 linkuse as main transcript	c.885+6G>A		splice_donor_region_variant, intron_variant		ENST00000375442.8	NP_071400.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TSPYL2	ENST00000375442.8 linkuse as main transcript	c.885+6G>A		splice_donor_region_variant, intron_variant		1	NM_022117.4	ENSP00000364591	P1

Frequencies

GnomAD3 genomes

AF:

0.00591

AC:

652

AN:

110303

Hom.:

Cov.:

AF XY:

0.00467

AC XY:

152

AN XY:

32537

show subpopulations

Gnomad AFR

AF:

0.00143

Gnomad AMI

AF:

0.00442

Gnomad AMR

AF:

0.00357

Gnomad ASJ

AF:

0.00873

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000784

Gnomad FIN

AF:

0.00514

Gnomad MID

AF:

0.00840

Gnomad NFE

AF:

0.00962

Gnomad OTH

AF:

0.00272

GnomAD3 exomes

AF:

0.00727

AC:

1302

AN:

179064

Hom.:

AF XY:

0.00714

AC XY:

455

AN XY:

63728

show subpopulations

Gnomad AFR exome

AF:

0.000838

Gnomad AMR exome

AF:

0.00737

Gnomad ASJ exome

AF:

0.0107

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00323

Gnomad FIN exome

AF:

0.00552

Gnomad NFE exome

AF:

0.0102

Gnomad OTH exome

AF:

0.0134

GnomAD4 exome

AF:

0.00918

AC:

10046

AN:

1094448

Hom.:

Cov.:

AF XY:

0.00891

AC XY:

3210

AN XY:

360146

show subpopulations

Gnomad4 AFR exome

AF:

0.00114

Gnomad4 AMR exome

AF:

0.00706

Gnomad4 ASJ exome

AF:

0.00979

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00412

Gnomad4 FIN exome

AF:

0.00551

Gnomad4 NFE exome

AF:

0.0105

Gnomad4 OTH exome

AF:

0.00699

GnomAD4 genome

AF:

0.00591

AC:

652

AN:

110356

Hom.:

Cov.:

AF XY:

0.00466

AC XY:

152

AN XY:

32600

show subpopulations

Gnomad4 AFR

AF:

0.00142

Gnomad4 AMR

AF:

0.00356

Gnomad4 ASJ

AF:

0.00873

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000787

Gnomad4 FIN

AF:

0.00514

Gnomad4 NFE

AF:

0.00962

Gnomad4 OTH

AF:

0.00268

Alfa

AF:

0.00723

Hom.:

Bravo

AF:

0.00573

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Nov 16, 2017	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.59

CADD

Benign

DANN

Benign

0.87

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.000032

dbscSNV1_RF

Benign

0.0

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over