Genetic Variant TBX2-AS1:n.458C>G (chr17-61399149-G-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000590421.2(TBX2-AS1):n.458C>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0873 in 152,320 control chromosomes in the GnomAD database, including 839 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 0.087 ( 839 hom., cov: 33)

Exomes 𝑓: 0.037 ( 0 hom. )

Consequence

TBX2-AS1
ENST00000590421.2 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.838

Publications

4 publications found

Variant links:

Genes affected

TBX2-AS1 (HGNC:50355): (TBX2 antisense RNA 1)

TBX2-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=-0.74).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.279 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
TBX2-AS1	NR_125749.1 link	n.458C>G	non_coding_transcript_exon_variant	Exon 1 of 2
TBX2-AS1	NR_125750.1 link	n.368+90C>G	intron_variant	Intron 1 of 2
TBX2-AS1	NR_125751.1 link	n.368+90C>G	intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
TBX2-AS1	ENST00000590421.2 link	n.458C>G	non_coding_transcript_exon_variant	Exon 1 of 2	2
TBX2-AS1	ENST00000585765.1 link	n.28+1067C>G	intron_variant	Intron 1 of 3	5
TBX2-AS1	ENST00000586706.6 link	n.91+90C>G	intron_variant	Intron 1 of 3	3

Frequencies

GnomAD3 genomes

AF:

0.0872

AC:

13263

AN:

152120

Hom.:

831

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0751

Gnomad AMI

AF:

0.0395

Gnomad AMR

AF:

0.169

Gnomad ASJ

AF:

0.0476

Gnomad EAS

AF:

0.291

Gnomad SAS

AF:

0.126

Gnomad FIN

AF:

0.110

Gnomad MID

AF:

0.0601

Gnomad NFE

AF:

0.0572

Gnomad OTH

AF:

0.0873

GnomAD4 exome

AF:

0.0366

AC:

AN:

Hom.:

Cov.:

AF XY:

0.0455

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.0395

AC:

AN:

Other (OTH)

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.642

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.0873

AC:

13296

AN:

152238

Hom.:

839

Cov.:

AF XY:

0.0927

AC XY:

6903

AN XY:

74440

show subpopulations

African (AFR)

AF:

0.0752

AC:

3123

AN:

41556

American (AMR)

AF:

0.170

AC:

2605

AN:

15300

Ashkenazi Jewish (ASJ)

AF:

0.0476

AC:

165

AN:

3470

East Asian (EAS)

AF:

0.292

AC:

1503

AN:

5152

South Asian (SAS)

AF:

0.126

AC:

608

AN:

4820

European-Finnish (FIN)

AF:

0.110

AC:

1166

AN:

10616

Middle Eastern (MID)

AF:

0.0646

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0572

AC:

3889

AN:

68012

Other (OTH)

AF:

0.0864

AC:

182

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

632

1263

1895

2526

3158

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

152

304

456

608

760

<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:

0.0687

Hom.:

Bravo

AF:

0.0913

Asia WGS

AF:

0.177

AC:

614

AN:

3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.74

CADD

Benign

7.8

(source)

DANN

Benign

0.64

PhyloP100

0.84

RBP_binding_hub_radar

0.97

RBP_regulation_power_radar

2.8

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