dbSNP rs2076537: TSBP1:c.260-98C>T (chr6-32349858-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001286474.2(TSBP1):c.260-98C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.385 in 1,347,764 control chromosomes in the GnomAD database, including 103,886 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.42 ( 14395 hom., cov: 32)

Exomes 𝑓: 0.38 ( 89491 hom. )

Consequence

TSBP1
NM_001286474.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.299

Publications

33 publications found

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 was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.539 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TSBP1	NM_001286474.2 link	c.260-98C>T		intron_variant	Intron 8 of 25	ENST00000533191.6	NP_001273403.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TSBP1	ENST00000533191.6 link	c.260-98C>T		intron_variant	Intron 8 of 25	1	NM_001286474.2	ENSP00000431199.1		Q5SRN2-3

Frequencies

GnomAD3 genomes

AF:

0.421

AC:

64007

AN:

151864

Hom.:

14371

Cov.:

show subpopulations

Gnomad AFR

AF:

0.545

Gnomad AMI

AF:

0.492

Gnomad AMR

AF:

0.302

Gnomad ASJ

AF:

0.222

Gnomad EAS

AF:

0.412

Gnomad SAS

AF:

0.435

Gnomad FIN

AF:

0.541

Gnomad MID

AF:

0.272

Gnomad NFE

AF:

0.365

Gnomad OTH

AF:

0.382

GnomAD2 exomes

AF:

0.375

AC:

92017

AN:

245454

AF XY:

0.375

show subpopulations

Gnomad AFR exome

AF:

0.556

Gnomad AMR exome

AF:

0.262

Gnomad ASJ exome

AF:

0.233

Gnomad EAS exome

AF:

0.393

Gnomad FIN exome

AF:

0.526

Gnomad NFE exome

AF:

0.361

Gnomad OTH exome

AF:

0.355

GnomAD4 exome

AF:

0.381

AC:

455408

AN:

1195782

Hom.:

89491

Cov.:

AF XY:

0.380

AC XY:

230948

AN XY:

607790

show subpopulations

African (AFR)

AF:

0.557

AC:

15777

AN:

28336

American (AMR)

AF:

0.265

AC:

11752

AN:

44274

Ashkenazi Jewish (ASJ)

AF:

0.235

AC:

5737

AN:

24448

East Asian (EAS)

AF:

0.492

AC:

18921

AN:

38422

South Asian (SAS)

AF:

0.393

AC:

31675

AN:

80530

European-Finnish (FIN)

AF:

0.524

AC:

27277

AN:

52090

Middle Eastern (MID)

AF:

0.262

AC:

1382

AN:

5278

European-Non Finnish (NFE)

AF:

0.372

AC:

323963

AN:

870932

Other (OTH)

AF:

0.368

AC:

18924

AN:

51472

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

14499

28998

43497

57996

72495

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

9314

18628

27942

37256

46570

<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

AF:

0.422

AC:

64073

AN:

151982

Hom.:

14395

Cov.:

AF XY:

0.426

AC XY:

31670

AN XY:

74296

show subpopulations

African (AFR)

AF:

0.545

AC:

22599

AN:

41432

American (AMR)

AF:

0.301

AC:

4600

AN:

15270

Ashkenazi Jewish (ASJ)

AF:

0.222

AC:

769

AN:

3466

East Asian (EAS)

AF:

0.413

AC:

2137

AN:

5180

South Asian (SAS)

AF:

0.434

AC:

2096

AN:

4826

European-Finnish (FIN)

AF:

0.541

AC:

5706

AN:

10542

Middle Eastern (MID)

AF:

0.289

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.365

AC:

24826

AN:

67956

Other (OTH)

AF:

0.383

AC:

808

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1825

3649

5474

7298

9123

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

584

1168

1752

2336

2920

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.378

Hom.:

26011

Bravo

AF:

0.405

Asia WGS

AF:

0.413

AC:

1436

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

3.2

(source)

DANN

Benign

0.50

PhyloP100

-0.30

Mutation Taster

=100/0

polymorphism (auto)

(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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over