dbSNP rs12891257: TRA:n.22393232C>T (chr14-22393232-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 variant allele was found at a frequency of 0.0611 in 150,890 control chromosomes in the GnomAD database, including 396 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 0.061 ( 396 hom., cov: 25)

Consequence

TRA
intragenic

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.441

Publications

3 publications found

Variant links:

Genes affected

TRA (HGNC:12027):

TRA links:

TRD-AS1 (HGNC:56197): (TRD antisense RNA 1)

TRD-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=-0.86).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0958 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
TRA		n.22393232C>T	intragenic_variant
TRD-AS1	NR_148361.1 link	n.226-10827G>A	intron_variant	Intron 2 of 4
TRD-AS1	NR_148362.1 link	n.289+7812G>A	intron_variant	Intron 3 of 5

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
TRD-AS1	ENST00000514473.2 link	n.226-10827G>A	intron_variant	Intron 2 of 2	2
TRD-AS1	ENST00000541008.6 link	n.276+7812G>A	intron_variant	Intron 3 of 5	4
TRD-AS1	ENST00000545670.5 link	n.275+7812G>A	intron_variant	Intron 3 of 3	4

Frequencies

GnomAD3 genomes

AF:

0.0611

AC:

9213

AN:

150772

Hom.:

396

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0162

Gnomad AMI

AF:

0.0143

Gnomad AMR

AF:

0.0470

Gnomad ASJ

AF:

0.0767

Gnomad EAS

AF:

0.00135

Gnomad SAS

AF:

0.102

Gnomad FIN

AF:

0.0609

Gnomad MID

AF:

0.0411

Gnomad NFE

AF:

0.0930

Gnomad OTH

AF:

0.0597

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

GnomAD4 genome

AF:

0.0611

AC:

9215

AN:

150890

Hom.:

396

Cov.:

AF XY:

0.0605

AC XY:

4457

AN XY:

73676

show subpopulations

African (AFR)

AF:

0.0162

AC:

662

AN:

40950

American (AMR)

AF:

0.0469

AC:

705

AN:

15034

Ashkenazi Jewish (ASJ)

AF:

0.0767

AC:

266

AN:

3466

East Asian (EAS)

AF:

0.00135

AC:

AN:

5178

South Asian (SAS)

AF:

0.103

AC:

491

AN:

4750

European-Finnish (FIN)

AF:

0.0609

AC:

637

AN:

10454

Middle Eastern (MID)

AF:

0.0476

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0929

AC:

6297

AN:

67756

Other (OTH)

AF:

0.0586

AC:

123

AN:

2098

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

410

819

1229

1638

2048

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

110

220

330

440

550

<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:

0.0786

Hom.:

366

Bravo

AF:

0.0552

Asia WGS

AF:

0.0380

AC:

131

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

2.3

(source)

DANN

Benign

0.58

PhyloP100

-0.44

Mutation Taster

=100/0

polymorphism

(source)

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