Variant chr6-32293475-T-G 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.1192A>C(p.Lys398Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.097 in 1,612,968 control chromosomes in the GnomAD database, including 9,852 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/17 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 ( 456 hom., cov: 31)

Exomes 𝑓: 0.10 ( 9396 hom. )

Consequence

TSBP1
NM_001286474.2 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.268

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=0.0019672513).

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	UniProt
TSBP1	NM_001286474.2 linkuse as main transcript	c.1192A>C	p.Lys398Gln	missense_variant	26/26	ENST00000533191.6
TSBP1-AS1	NR_136245.1 linkuse as main transcript	n.242+38061T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TSBP1	ENST00000533191.6 linkuse as main transcript	c.1192A>C	p.Lys398Gln	missense_variant	26/26	1	NM_001286474.2	A2	Q5SRN2-3
TSBP1-AS1	ENST00000645134.1 linkuse as main transcript	n.87+38061T>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.0626

AC:

9525

AN:

152118

Hom.:

456

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:

0.0842

Gnomad MID

AF:

0.0190

Gnomad NFE

AF:

0.106

Gnomad OTH

AF:

0.0470

GnomAD3 exomes

AF:

0.0595

AC:

14684

AN:

246618

Hom.:

777

AF XY:

0.0587

AC XY:

7880

AN XY:

134330

show subpopulations

Gnomad AFR exome

AF:

0.0162

Gnomad AMR exome

AF:

0.0219

Gnomad ASJ exome

AF:

0.0363

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.0000658

Gnomad FIN exome

AF:

0.0818

Gnomad NFE exome

AF:

0.101

Gnomad OTH exome

AF:

0.0609

GnomAD4 exome

AF:

0.101

AC:

146917

AN:

1460732

Hom.:

9396

Cov.:

AF XY:

0.0970

AC XY:

70493

AN XY:

726680

show subpopulations

Gnomad4 AFR exome

AF:

0.0158

Gnomad4 AMR exome

AF:

0.0226

Gnomad4 ASJ exome

AF:

0.0397

Gnomad4 EAS exome

AF:

0.000126

Gnomad4 SAS exome

AF:

0.000232

Gnomad4 FIN exome

AF:

0.0857

Gnomad4 NFE exome

AF:

0.121

Gnomad4 OTH exome

AF:

0.0864

GnomAD4 genome

AF:

0.0625

AC:

9522

AN:

152236

Hom.:

456

Cov.:

AF XY:

0.0582

AC XY:

4332

AN XY:

74434

show subpopulations

Gnomad4 AFR

AF:

0.0164

Gnomad4 AMR

AF:

0.0286

Gnomad4 ASJ

AF:

0.0380

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000207

Gnomad4 FIN

AF:

0.0842

Gnomad4 NFE

AF:

0.106

Gnomad4 OTH

AF:

0.0465

Alfa

AF:

0.0906

Hom.:

1525

Bravo

AF:

0.0571

TwinsUK

AF:

0.126

AC:

468

ALSPAC

AF:

0.125

AC:

483

ESP6500AA

AF:

0.0222

AC:

ESP6500EA

AF:

0.103

AC:

558

ExAC

AF:

0.0596

AC:

7042

Asia WGS

AF:

0.00462

AC:

AN:

3478

EpiCase

AF:

0.0930

EpiControl

AF:

0.0865

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.23

BayesDel_addAF

Benign

-0.69

BayesDel_noAF

Benign

-0.65

CADD

Benign

2.4

DANN

Benign

0.95

Eigen

Benign

-0.97

Eigen_PC

Benign

-1.2

FATHMM_MKL

Benign

0.018

LIST_S2

Benign

0.39

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

MetaRNN

Benign

0.0020

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

MetaSVM

Benign

-1.0

MutationTaster

Benign

1.0

N;N;N;N;N;N

PROVEAN

Benign

-2.0

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

REVEL

Benign

0.036

Sift

Uncertain

0.012

D;D;D;D;.;D;D;.

Sift4G

Benign

0.20

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

Vest4

0.15

MPC

1.1

ClinPred

0.029

GERP RS

-2.1

gMVP

0.031

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over