Genetic Variant TBX2-AS1:n.131G>A (chr17-61394011-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 ENST00000592377.2(TBX2-AS1):n.131G>A 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 0.142 in 152,238 control chromosomes in the GnomAD database, including 2,468 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 ( 2468 hom., cov: 33)

Exomes 𝑓: 0.034 ( 0 hom. )

Consequence

TBX2-AS1
ENST00000592377.2 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.31

Publications

5 publications found

Variant links:

COSMIC-nc: COSV66769912

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=-0.68).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.316 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
TBX2-AS1	NR_125749.1 link	n.571-264G>A	intron_variant	Intron 1 of 1
TBX2-AS1	NR_125750.1 link	n.486-264G>A	intron_variant	Intron 2 of 2
TBX2-AS1	NR_125751.1 link	n.369-264G>A	intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
TBX2-AS1	ENST00000592377.2 link	n.131G>A	non_coding_transcript_exon_variant	Exon 1 of 2	2
TBX2-AS1	ENST00000585765.1 link	n.28+6205G>A	intron_variant	Intron 1 of 3	5
TBX2-AS1	ENST00000586706.6 link	n.449-264G>A	intron_variant	Intron 3 of 3	3

Frequencies

GnomAD3 genomes

AF:

0.142

AC:

21621

AN:

152060

Hom.:

2465

Cov.:

show subpopulations

Gnomad AFR

AF:

0.279

Gnomad AMI

AF:

0.00987

Gnomad AMR

AF:

0.193

Gnomad ASJ

AF:

0.0377

Gnomad EAS

AF:

0.330

Gnomad SAS

AF:

0.184

Gnomad FIN

AF:

0.0609

Gnomad MID

AF:

0.0759

Gnomad NFE

AF:

0.0517

Gnomad OTH

AF:

0.108

GnomAD4 exome

AF:

0.0345

AC:

AN:

Hom.:

Cov.:

AF XY:

0.0556

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.00

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.0435

AC:

AN:

Other (OTH)

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.550

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.142

AC:

21650

AN:

152180

Hom.:

2468

Cov.:

AF XY:

0.144

AC XY:

10725

AN XY:

74388

show subpopulations

African (AFR)

AF:

0.279

AC:

11566

AN:

41500

American (AMR)

AF:

0.193

AC:

2949

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.0377

AC:

131

AN:

3472

East Asian (EAS)

AF:

0.329

AC:

1695

AN:

5148

South Asian (SAS)

AF:

0.184

AC:

886

AN:

4828

European-Finnish (FIN)

AF:

0.0609

AC:

646

AN:

10612

Middle Eastern (MID)

AF:

0.0612

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0518

AC:

3520

AN:

68018

Other (OTH)

AF:

0.109

AC:

230

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

879

1758

2636

3515

4394

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

230

460

690

920

1150

<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:

0.0905

Hom.:

2804

Bravo

AF:

0.160

Asia WGS

AF:

0.266

AC:

922

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.68

CADD

Benign

(source)

DANN

Benign

0.80

PhyloP100

1.3

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

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over