Variant 11-76795646-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_015516.4(TSKU):c.30C>T(p.Ala10=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00303 in 1,613,004 control chromosomes in the GnomAD database, including 32 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0023 ( 3 hom., cov: 33)

Exomes 𝑓: 0.0031 ( 29 hom. )

Consequence

TSKU
NM_015516.4 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.338

Variant links:

Genes affected

TSKU (HGNC:28850): (tsukushi, small leucine rich proteoglycan) Predicted to enable transforming growth factor beta binding activity. Predicted to be involved in several processes, including animal organ development; cholesterol efflux; and cholesterol homeostasis. Predicted to act upstream of or within several processes, including ciliary body morphogenesis; negative regulation of Wnt signaling pathway; and telencephalon development. Predicted to be located in extracellular space. [provided by Alliance of Genome Resources, Apr 2022]

TSKU links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.66).

BP6

Variant 11-76795646-C-T is Benign according to our data. Variant chr11-76795646-C-T is described in ClinVar as [Benign]. Clinvar id is 2642174.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-0.338 with no splicing effect.

BS2

High AC in GnomAd4 at 346 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TSKU	NM_015516.4 linkuse as main transcript	c.30C>T	p.Ala10=	synonymous_variant	2/2	ENST00000333090.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TSKU	ENST00000333090.5 linkuse as main transcript	c.30C>T	p.Ala10=	synonymous_variant	2/2	1	NM_015516.4	P1

Frequencies

GnomAD3 genomes

AF:

0.00226

AC:

344

AN:

152194

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000458

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00216

Gnomad ASJ

AF:

0.00144

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.0147

Gnomad FIN

AF:

0.00132

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00290

Gnomad OTH

AF:

0.00239

GnomAD3 exomes

AF:

0.00352

AC:

881

AN:

249932

Hom.:

AF XY:

0.00431

AC XY:

583

AN XY:

135306

show subpopulations

Gnomad AFR exome

AF:

0.000559

Gnomad AMR exome

AF:

0.00139

Gnomad ASJ exome

AF:

0.00269

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.0131

Gnomad FIN exome

AF:

0.00210

Gnomad NFE exome

AF:

0.00297

Gnomad OTH exome

AF:

0.00278

GnomAD4 exome

AF:

0.00311

AC:

4540

AN:

1460692

Hom.:

Cov.:

AF XY:

0.00348

AC XY:

2528

AN XY:

726674

show subpopulations

Gnomad4 AFR exome

AF:

0.000597

Gnomad4 AMR exome

AF:

0.00152

Gnomad4 ASJ exome

AF:

0.00325

Gnomad4 EAS exome

AF:

0.000227

Gnomad4 SAS exome

AF:

0.0136

Gnomad4 FIN exome

AF:

0.00168

Gnomad4 NFE exome

AF:

0.00257

Gnomad4 OTH exome

AF:

0.00330

GnomAD4 genome

AF:

0.00227

AC:

346

AN:

152312

Hom.:

Cov.:

AF XY:

0.00235

AC XY:

175

AN XY:

74468

show subpopulations

Gnomad4 AFR

AF:

0.000481

Gnomad4 AMR

AF:

0.00216

Gnomad4 ASJ

AF:

0.00144

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.0149

Gnomad4 FIN

AF:

0.00132

Gnomad4 NFE

AF:

0.00290

Gnomad4 OTH

AF:

0.00236

Alfa

AF:

0.00254

Hom.:

Bravo

AF:

0.00175

Asia WGS

AF:

0.00318

AC:

AN:

3478

EpiCase

AF:

0.00322

EpiControl

AF:

0.00379

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Nov 01, 2022

TSKU: BP4, BP7, BS1, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.66

CADD

Benign

2.3

DANN

Benign

0.78

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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

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