dbSNP rs9268499: TSBP1-AS1:n.*155G>A (chr6-32407918-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 ENST00000642577.1(TSBP1-AS1):n.*155G>A variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.297 in 151,964 control chromosomes in the GnomAD database, including 6,957 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 0.30 ( 6957 hom., cov: 32)

Consequence

TSBP1-AS1
ENST00000642577.1 downstream_gene

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.913

Publications

26 publications found

Variant links:

Genes affected

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=-1.02).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.438 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TSBP1-AS1	NR_136245.1 link	n.*188G>A		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	Effect
TSBP1-AS1	ENST00000642577.1 link	n.*155G>A	downstream_gene_variant
TSBP1-AS1	ENST00000645134.1 link	n.*155G>A	downstream_gene_variant
TSBP1-AS1	ENST00000645167.1 link	n.*244G>A	downstream_gene_variant

Frequencies

GnomAD3 genomes

AF:

0.297

AC:

45115

AN:

151846

Hom.:

6956

Cov.:

show subpopulations

Gnomad AFR

AF:

0.277

Gnomad AMI

AF:

0.239

Gnomad AMR

AF:

0.324

Gnomad ASJ

AF:

0.379

Gnomad EAS

AF:

0.452

Gnomad SAS

AF:

0.445

Gnomad FIN

AF:

0.213

Gnomad MID

AF:

0.253

Gnomad NFE

AF:

0.291

Gnomad OTH

AF:

0.289

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

GnomAD4 genome

AF:

0.297

AC:

45140

AN:

151964

Hom.:

6957

Cov.:

AF XY:

0.298

AC XY:

22117

AN XY:

74308

show subpopulations

African (AFR)

AF:

0.277

AC:

11468

AN:

41406

American (AMR)

AF:

0.324

AC:

4951

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.379

AC:

1314

AN:

3468

East Asian (EAS)

AF:

0.453

AC:

2344

AN:

5172

South Asian (SAS)

AF:

0.445

AC:

2147

AN:

4830

European-Finnish (FIN)

AF:

0.213

AC:

2244

AN:

10548

Middle Eastern (MID)

AF:

0.252

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.291

AC:

19777

AN:

67940

Other (OTH)

AF:

0.287

AC:

604

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

1585

3170

4754

6339

7924

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

466

932

1398

1864

2330

<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:

0.304

Hom.:

13586

Bravo

AF:

0.308

Asia WGS

AF:

0.415

AC:

1441

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.98

(source)

DANN

Benign

0.65

PhyloP100

-0.91

Splicing

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over