dbSNP rs2273017: TSBP1:c.100+44C>T (chr6-32369853-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.100+44C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.577 in 1,213,680 control chromosomes in the GnomAD database, including 206,252 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 0.50 ( 20856 hom., cov: 31)

Exomes 𝑓: 0.59 ( 185396 hom. )

Consequence

TSBP1
NM_001286474.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.28

Publications

59 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=-0.81).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.608 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TSBP1	NM_001286474.2 link	c.100+44C>T		intron_variant	Intron 2 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.100+44C>T		intron_variant	Intron 2 of 25	1	NM_001286474.2	ENSP00000431199.1		Q5SRN2-3

Frequencies

GnomAD3 genomes

AF:

0.504

AC:

76497

AN:

151856

Hom.:

20835

Cov.:

show subpopulations

Gnomad AFR

AF:

0.277

Gnomad AMI

AF:

0.607

Gnomad AMR

AF:

0.540

Gnomad ASJ

AF:

0.633

Gnomad EAS

AF:

0.626

Gnomad SAS

AF:

0.597

Gnomad FIN

AF:

0.562

Gnomad MID

AF:

0.623

Gnomad NFE

AF:

0.600

Gnomad OTH

AF:

0.512

GnomAD2 exomes

AF:

0.589

AC:

144967

AN:

246278

AF XY:

0.595

show subpopulations

Gnomad AFR exome

AF:

0.279

Gnomad AMR exome

AF:

0.629

Gnomad ASJ exome

AF:

0.636

Gnomad EAS exome

AF:

0.621

Gnomad FIN exome

AF:

0.560

Gnomad NFE exome

AF:

0.608

Gnomad OTH exome

AF:

0.569

GnomAD4 exome

AF:

0.587

AC:

623189

AN:

1061704

Hom.:

185396

Cov.:

AF XY:

0.590

AC XY:

322402

AN XY:

546028

show subpopulations

African (AFR)

AF:

0.279

AC:

7153

AN:

25656

American (AMR)

AF:

0.619

AC:

27375

AN:

44222

Ashkenazi Jewish (ASJ)

AF:

0.631

AC:

14957

AN:

23686

East Asian (EAS)

AF:

0.562

AC:

21298

AN:

37884

South Asian (SAS)

AF:

0.614

AC:

47953

AN:

78072

European-Finnish (FIN)

AF:

0.561

AC:

29266

AN:

52128

Middle Eastern (MID)

AF:

0.636

AC:

3163

AN:

4970

European-Non Finnish (NFE)

AF:

0.594

AC:

444594

AN:

747946

Other (OTH)

AF:

0.582

AC:

27430

AN:

47140

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.486

Heterozygous variant carriers

12693

25386

38078

50771

63464

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

9838

19676

29514

39352

49190

<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:

0.504

AC:

76550

AN:

151976

Hom.:

20856

Cov.:

AF XY:

0.504

AC XY:

37436

AN XY:

74278

show subpopulations

African (AFR)

AF:

0.278

AC:

11501

AN:

41430

American (AMR)

AF:

0.541

AC:

8267

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.633

AC:

2195

AN:

3470

East Asian (EAS)

AF:

0.626

AC:

3230

AN:

5158

South Asian (SAS)

AF:

0.596

AC:

2872

AN:

4820

European-Finnish (FIN)

AF:

0.562

AC:

5930

AN:

10548

Middle Eastern (MID)

AF:

0.612

AC:

180

AN:

294

European-Non Finnish (NFE)

AF:

0.600

AC:

40744

AN:

67952

Other (OTH)

AF:

0.512

AC:

1080

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

1770

3540

5309

7079

8849

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

686

1372

2058

2744

3430

<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:

0.588

Hom.:

97762

Bravo

AF:

0.493

Asia WGS

AF:

0.566

AC:

1971

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

1.7

(source)

DANN

Benign

0.52

PhyloP100

-1.3

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