dbSNP rs2286524: TBX2-AS1:n.49G>A (chr17-61399531-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 ENST00000589814.6(TBX2-AS1):n.49G>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 0.0926 in 152,298 control chromosomes in the GnomAD database, including 906 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 0.093 ( 906 hom., cov: 33)

Exomes 𝑓: 0.048 ( 0 hom. )

Consequence

TBX2-AS1
ENST00000589814.6 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.19

Publications

4 publications found

Variant links:

COSMIC-nc: COSV107270566

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=-0.53).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.278 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
TBX2-AS1	NR_125749.1 link	n.76G>A	non_coding_transcript_exon_variant	Exon 1 of 2
TBX2-AS1	NR_125750.1 link	n.76G>A	non_coding_transcript_exon_variant	Exon 1 of 3
TBX2-AS1	NR_125751.1 link	n.76G>A	non_coding_transcript_exon_variant	Exon 1 of 2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
TBX2-AS1	ENST00000589814.6 link	n.49G>A	non_coding_transcript_exon_variant	Exon 1 of 3	3
TBX2-AS1	ENST00000590421.2 link	n.76G>A	non_coding_transcript_exon_variant	Exon 1 of 2	2
TBX2-AS1	ENST00000591313.8 link	n.79G>A	non_coding_transcript_exon_variant	Exon 1 of 2	2

Frequencies

GnomAD3 genomes

AF:

0.0924

AC:

14053

AN:

152066

Hom.:

897

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0946

Gnomad AMI

AF:

0.0395

Gnomad AMR

AF:

0.171

Gnomad ASJ

AF:

0.0478

Gnomad EAS

AF:

0.289

Gnomad SAS

AF:

0.124

Gnomad FIN

AF:

0.109

Gnomad MID

AF:

0.0637

Gnomad NFE

AF:

0.0567

Gnomad OTH

AF:

0.0898

GnomAD4 exome

AF:

0.0484

AC:

AN:

124

Hom.:

Cov.:

AF XY:

0.0510

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

0.500

AC:

AN:

South Asian (SAS)

AF:

0.00

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.0431

AC:

AN:

116

Other (OTH)

AF:

0.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.458

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.0926

AC:

14092

AN:

152174

Hom.:

906

Cov.:

AF XY:

0.0979

AC XY:

7284

AN XY:

74386

show subpopulations

African (AFR)

AF:

0.0948

AC:

3937

AN:

41538

American (AMR)

AF:

0.173

AC:

2639

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.0478

AC:

166

AN:

3470

East Asian (EAS)

AF:

0.290

AC:

1485

AN:

5124

South Asian (SAS)

AF:

0.125

AC:

603

AN:

4834

European-Finnish (FIN)

AF:

0.109

AC:

1161

AN:

10604

Middle Eastern (MID)

AF:

0.0685

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.0567

AC:

3857

AN:

67992

Other (OTH)

AF:

0.0888

AC:

188

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.491

Heterozygous variant carriers

624

1248

1873

2497

3121

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

160

320

480

640

800

<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:

0.0721

Hom.:

Bravo

AF:

0.0978

Asia WGS

AF:

0.178

AC:

616

AN:

3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.53

CADD

Benign

(source)

DANN

Benign

0.96

PhyloP100

-1.2

PromoterAI

-0.0062

Neutral

(source)

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.8

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