Genetic Variant NM_001286474.2: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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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