Variant 6-32291750-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000442822.6(TSBP1):c.1359+1537C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.828 in 152,138 control chromosomes in the GnomAD database, including 52,284 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 0.83 ( 52284 hom., cov: 31)

Consequence

TSBP1
ENST00000442822.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0720

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 (BayesDel_noAF=-0.95).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.898 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect
TSBP1-AS1	NR_136245.1 linkuse as main transcript	n.242+36336G>A	intron_variant, non_coding_transcript_variant
TSBP1-AS1	NR_136244.1 linkuse as main transcript	n.440+28941G>A	intron_variant, non_coding_transcript_variant
TSBP1-AS1	NR_136246.1 linkuse as main transcript	n.242+36336G>A	intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TSBP1-AS1	ENST00000645134.1 linkuse as main transcript	n.87+36336G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.828

AC:

125889

AN:

152020

Hom.:

52235

Cov.:

show subpopulations

Gnomad AFR

AF:

0.787

Gnomad AMI

AF:

0.912

Gnomad AMR

AF:

0.845

Gnomad ASJ

AF:

0.861

Gnomad EAS

AF:

0.906

Gnomad SAS

AF:

0.920

Gnomad FIN

AF:

0.861

Gnomad MID

AF:

0.867

Gnomad NFE

AF:

0.829

Gnomad OTH

AF:

0.829

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.828

AC:

125995

AN:

152138

Hom.:

52284

Cov.:

AF XY:

0.831

AC XY:

61816

AN XY:

74382

show subpopulations

Gnomad4 AFR

AF:

0.787

Gnomad4 AMR

AF:

0.845

Gnomad4 ASJ

AF:

0.861

Gnomad4 EAS

AF:

0.907

Gnomad4 SAS

AF:

0.920

Gnomad4 FIN

AF:

0.861

Gnomad4 NFE

AF:

0.829

Gnomad4 OTH

AF:

0.830

Alfa

AF:

0.841

Hom.:

70728

Bravo

AF:

0.824

Asia WGS

AF:

0.882

AC:

3068

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

2.3

DANN

Benign

0.68

Splicing

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