Variant 6-32355752-A-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.218-83T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.569 in 1,462,402 control chromosomes in the GnomAD database, including 240,000 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 0.52 ( 20759 hom., cov: 31)

Exomes 𝑓: 0.58 ( 219241 hom. )

Consequence

TSBP1
NM_001286474.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.926

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.87).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.576 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TSBP1	NM_001286474.2 link	c.218-83T>C		intron_variant		ENST00000533191.6	NP_001273403.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TSBP1	ENST00000533191.6 link	c.218-83T>C		intron_variant		1	NM_001286474.2	ENSP00000431199.1		Q5SRN2-3

Frequencies

GnomAD3 genomes

AF:

0.516

AC:

78270

AN:

151806

Hom.:

20738

Cov.:

show subpopulations

Gnomad AFR

AF:

0.394

Gnomad AMI

AF:

0.610

Gnomad AMR

AF:

0.545

Gnomad ASJ

AF:

0.623

Gnomad EAS

AF:

0.473

Gnomad SAS

AF:

0.561

Gnomad FIN

AF:

0.484

Gnomad MID

AF:

0.617

Gnomad NFE

AF:

0.581

Gnomad OTH

AF:

0.517

GnomAD4 exome

AF:

0.576

AC:

754497

AN:

1310478

Hom.:

219241

AF XY:

0.577

AC XY:

373882

AN XY:

647428

show subpopulations

Gnomad4 AFR exome

AF:

0.398

Gnomad4 AMR exome

AF:

0.623

Gnomad4 ASJ exome

AF:

0.616

Gnomad4 EAS exome

AF:

0.444

Gnomad4 SAS exome

AF:

0.600

Gnomad4 FIN exome

AF:

0.497

Gnomad4 NFE exome

AF:

0.584

Gnomad4 OTH exome

AF:

0.570

GnomAD4 genome

AF:

0.516

AC:

78340

AN:

151924

Hom.:

20759

Cov.:

AF XY:

0.511

AC XY:

37931

AN XY:

74244

show subpopulations

Gnomad4 AFR

AF:

0.394

Gnomad4 AMR

AF:

0.546

Gnomad4 ASJ

AF:

0.623

Gnomad4 EAS

AF:

0.473

Gnomad4 SAS

AF:

0.561

Gnomad4 FIN

AF:

0.484

Gnomad4 NFE

AF:

0.581

Gnomad4 OTH

AF:

0.516

Alfa

AF:

0.579

Hom.:

22644

Bravo

AF:

0.517

Asia WGS

AF:

0.492

AC:

1713

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

0.17

DANN

Benign

0.38

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