Genetic Variant TOB1-AS1:n.572-239A>G (chr17-50916911-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000803431.1(TOB1-AS1):n.572-239A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.327 in 151,836 control chromosomes in the GnomAD database, including 8,612 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 0.33 ( 8612 hom., cov: 32)

Consequence

TOB1-AS1
ENST00000803431.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0920

Publications

2 publications found

Variant links:

Genes affected

TOB1-AS1 (HGNC:44340): (TOB1 antisense RNA 1)

TOB1-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=-0.92).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.607 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
TOB1-AS1	ENST00000803431.1 link	n.572-239A>G	intron_variant	Intron 3 of 5
TOB1-AS1	ENST00000803432.1 link	n.794-239A>G	intron_variant	Intron 2 of 4
TOB1-AS1	ENST00000803433.1 link	n.586-239A>G	intron_variant	Intron 4 of 6

Frequencies

GnomAD3 genomes

AF:

0.327

AC:

49576

AN:

151718

Hom.:

8604

Cov.:

show subpopulations

Gnomad AFR

AF:

0.292

Gnomad AMI

AF:

0.258

Gnomad AMR

AF:

0.376

Gnomad ASJ

AF:

0.380

Gnomad EAS

AF:

0.625

Gnomad SAS

AF:

0.552

Gnomad FIN

AF:

0.373

Gnomad MID

AF:

0.364

Gnomad NFE

AF:

0.288

Gnomad OTH

AF:

0.353

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

GnomAD4 genome

AF:

0.327

AC:

49608

AN:

151836

Hom.:

8612

Cov.:

AF XY:

0.338

AC XY:

25040

AN XY:

74188

show subpopulations

African (AFR)

AF:

0.292

AC:

12068

AN:

41342

American (AMR)

AF:

0.377

AC:

5753

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.380

AC:

1320

AN:

3470

East Asian (EAS)

AF:

0.625

AC:

3212

AN:

5142

South Asian (SAS)

AF:

0.552

AC:

2663

AN:

4820

European-Finnish (FIN)

AF:

0.373

AC:

3928

AN:

10528

Middle Eastern (MID)

AF:

0.361

AC:

106

AN:

294

European-Non Finnish (NFE)

AF:

0.288

AC:

19563

AN:

67948

Other (OTH)

AF:

0.361

AC:

761

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

1682

3365

5047

6730

8412

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

498

996

1494

1992

2490

<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:

0.309

Hom.:

14850

Bravo

AF:

0.322

Asia WGS

AF:

0.579

AC:

2013

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

7.1

(source)

DANN

Benign

0.60

PhyloP100

-0.092

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