Genetic Variant TSBP1-AS1:n.169-276C>T (chr6-32389938-C-T) – 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.169-276C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.144 in 152,094 control chromosomes in the GnomAD database, including 1,705 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 0.14 ( 1705 hom., cov: 32)

Consequence

TSBP1-AS1
ENST00000642577.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.293

Publications

29 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=-0.93).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.146 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TSBP1-AS1	NR_136245.1 link	n.303-15516C>T		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
TSBP1-AS1	ENST00000642577.1 link	n.169-276C>T	intron_variant	Intron 2 of 5
TSBP1-AS1	ENST00000644884.2 link	n.869-276C>T	intron_variant	Intron 3 of 3
TSBP1-AS1	ENST00000645134.1 link	n.88-276C>T	intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes

AF:

0.145

AC:

21965

AN:

151976

Hom.:

1704

Cov.:

show subpopulations

Gnomad AFR

AF:

0.149

Gnomad AMI

AF:

0.231

Gnomad AMR

AF:

0.131

Gnomad ASJ

AF:

0.0343

Gnomad EAS

AF:

0.0439

Gnomad SAS

AF:

0.0854

Gnomad FIN

AF:

0.269

Gnomad MID

AF:

0.111

Gnomad NFE

AF:

0.142

Gnomad OTH

AF:

0.143

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

GnomAD4 genome

AF:

0.144

AC:

21973

AN:

152094

Hom.:

1705

Cov.:

AF XY:

0.148

AC XY:

10981

AN XY:

74350

show subpopulations

African (AFR)

AF:

0.149

AC:

6196

AN:

41480

American (AMR)

AF:

0.131

AC:

1999

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.0343

AC:

119

AN:

3472

East Asian (EAS)

AF:

0.0436

AC:

226

AN:

5186

South Asian (SAS)

AF:

0.0855

AC:

412

AN:

4820

European-Finnish (FIN)

AF:

0.269

AC:

2843

AN:

10560

Middle Eastern (MID)

AF:

0.105

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.142

AC:

9639

AN:

67968

Other (OTH)

AF:

0.141

AC:

298

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

949

1897

2846

3794

4743

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

224

448

672

896

1120

<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:

0.132

Hom.:

4927

Bravo

AF:

0.134

Asia WGS

AF:

0.0740

AC:

258

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

2.8

(source)

DANN

Benign

0.31

PhyloP100

-0.29

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