Genetic Variant ENST00000795402.1:n.151+15947G>A (chr6-133901115-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 ENST00000795402.1(TARID):n.151+15947G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.939 in 152,262 control chromosomes in the GnomAD database, including 67,210 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 0.94 ( 67210 hom., cov: 32)

Consequence

TARID
ENST00000795402.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.101

Publications

4 publications found

Variant links:

Genes affected

TARID (HGNC:50506): (TCF21 antisense RNA inducing promoter demethylation)

TARID 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=-0.96).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
TARID	ENST00000795402.1 link	n.151+15947G>A	intron_variant	Intron 1 of 5
TARID	ENST00000795414.1 link	n.208+15947G>A	intron_variant	Intron 2 of 5
TARID	ENST00000795415.1 link	n.163+36169G>A	intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes

AF:

0.939

AC:

142864

AN:

152144

Hom.:

67149

Cov.:

show subpopulations

Gnomad AFR

AF:

0.984

Gnomad AMI

AF:

0.897

Gnomad AMR

AF:

0.960

Gnomad ASJ

AF:

0.896

Gnomad EAS

AF:

0.886

Gnomad SAS

AF:

0.930

Gnomad FIN

AF:

0.903

Gnomad MID

AF:

0.921

Gnomad NFE

AF:

0.920

Gnomad OTH

AF:

0.940

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

GnomAD4 genome

AF:

0.939

AC:

142984

AN:

152262

Hom.:

67210

Cov.:

AF XY:

0.938

AC XY:

69834

AN XY:

74416

show subpopulations

African (AFR)

AF:

0.984

AC:

40898

AN:

41560

American (AMR)

AF:

0.960

AC:

14691

AN:

15298

Ashkenazi Jewish (ASJ)

AF:

0.896

AC:

3109

AN:

3470

East Asian (EAS)

AF:

0.886

AC:

4582

AN:

5170

South Asian (SAS)

AF:

0.930

AC:

4485

AN:

4822

European-Finnish (FIN)

AF:

0.903

AC:

9559

AN:

10588

Middle Eastern (MID)

AF:

0.915

AC:

269

AN:

294

European-Non Finnish (NFE)

AF:

0.920

AC:

62584

AN:

68034

Other (OTH)

AF:

0.941

AC:

1991

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.494

Heterozygous variant carriers

432

864

1296

1728

2160

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

910

1820

2730

3640

4550

<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:

0.928

Hom.:

8489

Bravo

AF:

0.947

Asia WGS

AF:

0.934

AC:

3249

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.96

CADD

Benign

2.2

(source)

DANN

Benign

0.41

PhyloP100

0.10

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