dbSNP rs1476781: TBX2-AS1:n.553A>G (chr17-61399054-T-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.553A>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 0.771 in 152,158 control chromosomes in the GnomAD database, including 45,450 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 0.77 ( 45444 hom., cov: 34)

Exomes 𝑓: 0.73 ( 6 hom. )

Consequence

TBX2-AS1
ENST00000590421.2 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0340

Publications

8 publications found

Variant links:

Genes affected

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

TBX2-AS1 links:

ENSG00000289926 (HGNC:):

ENSG00000289926 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=-0.89).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.78 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
TBX2-AS1	NR_125749.1 link	n.553A>G	non_coding_transcript_exon_variant	Exon 1 of 2
TBX2-AS1	NR_125750.1 link	n.368+185A>G	intron_variant	Intron 1 of 2
TBX2-AS1	NR_125751.1 link	n.368+185A>G	intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
TBX2-AS1	ENST00000590421.2 link	n.553A>G	non_coding_transcript_exon_variant	Exon 1 of 2	2
TBX2-AS1	ENST00000722645.1 link	n.401A>G	non_coding_transcript_exon_variant	Exon 2 of 3
TBX2-AS1	ENST00000722655.1 link	n.87A>G	non_coding_transcript_exon_variant	Exon 1 of 3

Frequencies

GnomAD3 genomes

AF:

0.771

AC:

117256

AN:

152022

Hom.:

45397

Cov.:

show subpopulations

Gnomad AFR

AF:

0.786

Gnomad AMI

AF:

0.808

Gnomad AMR

AF:

0.703

Gnomad ASJ

AF:

0.747

Gnomad EAS

AF:

0.690

Gnomad SAS

AF:

0.666

Gnomad FIN

AF:

0.835

Gnomad MID

AF:

0.737

Gnomad NFE

AF:

0.783

Gnomad OTH

AF:

0.755

GnomAD4 exome

AF:

0.727

AC:

AN:

Hom.:

Cov.:

AF XY:

0.643

AC XY:

AN XY:

show subpopulations

African (AFR)

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:

0.800

AC:

AN:

Other (OTH)

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.450

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.771

AC:

117362

AN:

152136

Hom.:

45444

Cov.:

AF XY:

0.771

AC XY:

57311

AN XY:

74370

show subpopulations

African (AFR)

AF:

0.787

AC:

32668

AN:

41528

American (AMR)

AF:

0.704

AC:

10765

AN:

15302

Ashkenazi Jewish (ASJ)

AF:

0.747

AC:

2595

AN:

3472

East Asian (EAS)

AF:

0.691

AC:

3542

AN:

5124

South Asian (SAS)

AF:

0.665

AC:

3207

AN:

4820

European-Finnish (FIN)

AF:

0.835

AC:

8844

AN:

10588

Middle Eastern (MID)

AF:

0.745

AC:

219

AN:

294

European-Non Finnish (NFE)

AF:

0.782

AC:

53196

AN:

67984

Other (OTH)

AF:

0.752

AC:

1589

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

1423

2846

4270

5693

7116

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

860

1720

2580

3440

4300

<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:

0.782

Hom.:

6003

Bravo

AF:

0.763

Asia WGS

AF:

0.680

AC:

2366

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

8.0

(source)

DANN

Benign

0.43

PhyloP100

-0.034

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