Variant rs1265754 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001286474.2(TSBP1):c.400A>T(p.Ile134Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0962 in 1,606,862 control chromosomes in the GnomAD database, including 9,765 homozygotes. In-silico tool predicts a benign outcome for this variant. 11/17 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.063 ( 461 hom., cov: 32)

Exomes 𝑓: 0.10 ( 9304 hom. )

Consequence

TSBP1
NM_001286474.2 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.961

Variant links:

Genes affected

TSBP1 (HGNC:13922): (testis expressed basic protein 1) Located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

TSBP1 links:

TSBP1-AS1 (HGNC:39756): (TSBP1 and BTNL2 antisense RNA 1)

TSBP1-AS1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0020620227).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.104 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TSBP1	NM_001286474.2 linkuse as main transcript	c.400A>T	p.Ile134Phe	missense_variant	14/26	ENST00000533191.6	NP_001273403.1
TSBP1-AS1	NR_136245.1 linkuse as main transcript	n.243-29865T>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TSBP1	ENST00000533191.6 linkuse as main transcript	c.400A>T	p.Ile134Phe	missense_variant	14/26	1	NM_001286474.2	ENSP00000431199	A2	Q5SRN2-3
TSBP1-AS1	ENST00000645134.1 linkuse as main transcript	n.88-54299T>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.0627

AC:

9547

AN:

152152

Hom.:

461

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0165

Gnomad AMI

AF:

0.0559

Gnomad AMR

AF:

0.0287

Gnomad ASJ

AF:

0.0380

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000207

Gnomad FIN

AF:

0.0848

Gnomad MID

AF:

0.0190

Gnomad NFE

AF:

0.106

Gnomad OTH

AF:

0.0455

GnomAD3 exomes

AF:

0.0587

AC:

14227

AN:

242528

Hom.:

745

AF XY:

0.0581

AC XY:

7694

AN XY:

132530

show subpopulations

Gnomad AFR exome

AF:

0.0162

Gnomad AMR exome

AF:

0.0217

Gnomad ASJ exome

AF:

0.0362

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.0000660

Gnomad FIN exome

AF:

0.0819

Gnomad NFE exome

AF:

0.100

Gnomad OTH exome

AF:

0.0613

GnomAD4 exome

AF:

0.0997

AC:

145081

AN:

1454592

Hom.:

9304

Cov.:

AF XY:

0.0963

AC XY:

69715

AN XY:

724088

show subpopulations

Gnomad4 AFR exome

AF:

0.0157

Gnomad4 AMR exome

AF:

0.0225

Gnomad4 ASJ exome

AF:

0.0395

Gnomad4 EAS exome

AF:

0.000101

Gnomad4 SAS exome

AF:

0.000232

Gnomad4 FIN exome

AF:

0.0857

Gnomad4 NFE exome

AF:

0.120

Gnomad4 OTH exome

AF:

0.0859

GnomAD4 genome

AF:

0.0627

AC:

9544

AN:

152270

Hom.:

461

Cov.:

AF XY:

0.0584

AC XY:

4348

AN XY:

74444

show subpopulations

Gnomad4 AFR

AF:

0.0165

Gnomad4 AMR

AF:

0.0286

Gnomad4 ASJ

AF:

0.0380

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000208

Gnomad4 FIN

AF:

0.0848

Gnomad4 NFE

AF:

0.106

Gnomad4 OTH

AF:

0.0450

Alfa

AF:

0.0846

Hom.:

447

Bravo

AF:

0.0571

TwinsUK

AF:

0.126

AC:

469

ALSPAC

AF:

0.125

AC:

483

ESP6500AA

AF:

0.0222

AC:

ESP6500EA

AF:

0.103

AC:

558

ExAC

AF:

0.0597

AC:

7033

Asia WGS

AF:

0.00462

AC:

AN:

3478

EpiCase

AF:

0.0927

EpiControl

AF:

0.0859

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Uncertain

0.50

BayesDel_addAF

Benign

-0.56

BayesDel_noAF

Benign

-0.47

CADD

Benign

DANN

Benign

0.95

Eigen

Benign

-0.048

Eigen_PC

Benign

-0.067

FATHMM_MKL

Benign

0.64

LIST_S2

Benign

0.60

T;.;T;T;T;T;T

MetaRNN

Benign

0.0021

T;T;T;T;T;T;T

MetaSVM

Benign

-0.95

MutationTaster

Benign

0.97

N;N;N;N;N;N

PROVEAN

Benign

-1.7

N;N;N;N;.;N;N

REVEL

Benign

0.061

Sift

Benign

0.071

T;T;T;T;.;T;T

Sift4G

Uncertain

0.048

D;D;D;T;D;D;D

Vest4

0.58

MPC

0.49

ClinPred

0.024

GERP RS

3.0

gMVP

0.054

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over