Genetic Variant NM_022117.4:c.280T>G (chrX-53082778-T-G) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_022117.4(TSPYL2):c.280T>G(p.Cys94Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000924 in 1,082,360 control chromosomes in the GnomAD database, with no homozygous occurrence. There are no hemizygote samples in GnomAD. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. C94R) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 22)

Exomes 𝑓: 9.2e-7 ( 0 hom. 0 hem. )

Consequence

TSPYL2
NM_022117.4 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.479

Publications

0 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 -2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (MetaRNN=0.022072226).

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.280T>G	p.Cys94Gly	missense	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.280T>G	p.Cys94Gly	missense	Exon 1 of 7	ENSP00000364591.4	Q9H2G4
TSPYL2	ENST00000912653.1		c.280T>G	p.Cys94Gly	missense	Exon 1 of 7	ENSP00000582712.1
TSPYL2	ENST00000887608.1		c.280T>G	p.Cys94Gly	missense	Exon 1 of 7	ENSP00000557667.1

Frequencies

GnomAD3 genomes

Cov.:

GnomAD2 exomes

AF:

0.00000678

AC:

AN:

147534

AF XY:

0.00

show subpopulations

Gnomad AFR exome

AF:

0.0000999

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

9.24e-7

AC:

AN:

1082360

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

352772

show subpopulations

African (AFR)

AF:

0.0000388

AC:

AN:

25779

American (AMR)

AF:

0.00

AC:

AN:

31787

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

18784

East Asian (EAS)

AF:

0.00

AC:

AN:

29774

South Asian (SAS)

AF:

0.00

AC:

AN:

52309

European-Finnish (FIN)

AF:

0.00

AC:

AN:

38900

Middle Eastern (MID)

AF:

0.00

AC:

AN:

4062

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

835560

Other (OTH)

AF:

0.00

AC:

AN:

45405

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.425

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

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

GnomAD4 genome

Cov.:

Alfa

AF:

0.00

Hom.:

ExAC

AF:

0.00000830

AC:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.047

BayesDel_addAF

Benign

-0.64

BayesDel_noAF

Benign

-0.95

CADD

Benign

0.16

(source)

DANN

Benign

0.63

DEOGEN2

Benign

0.17

FATHMM_MKL

Benign

0.0039

LIST_S2

Benign

0.53

M_CAP

Benign

0.0059

MetaRNN

Benign

0.022

MetaSVM

Benign

-0.98

MutationAssessor

Benign

-0.86

PhyloP100

-0.48

PrimateAI

Uncertain

0.50

PROVEAN

Benign

1.4

REVEL

Benign

0.019

Sift

Benign

1.0

Sift4G

Benign

0.56

Polyphen

0.0

Vest4

0.14

MutPred

0.32

Gain of disorder (P = 0.0263)

MVP

0.043

MPC

0.32

ClinPred

0.020

GERP RS

-0.74

PromoterAI

-0.025

Neutral

(source)

Varity_R

0.058

gMVP

0.083

Mutation Taster

=98/2

polymorphism

(source)

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

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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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over