dbSNP rs17116039: TRA:n.22284990A>G (chr14-22284990-A-G) – 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 0.264 in 151,010 control chromosomes in the GnomAD database, including 5,389 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 0.26 ( 5389 hom., cov: 26)

Consequence

TRA
intragenic

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.225

Publications

5 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=-0.89).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.288 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRA		n.22284990A>G		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TRD-AS1	ENST00000656379.1 link	n.271-83608T>C		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes

AF:

0.264

AC:

39855

AN:

150892

Hom.:

5379

Cov.:

show subpopulations

Gnomad AFR

AF:

0.243

Gnomad AMI

AF:

0.176

Gnomad AMR

AF:

0.260

Gnomad ASJ

AF:

0.226

Gnomad EAS

AF:

0.0913

Gnomad SAS

AF:

0.300

Gnomad FIN

AF:

0.284

Gnomad MID

AF:

0.217

Gnomad NFE

AF:

0.289

Gnomad OTH

AF:

0.259

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

GnomAD4 genome

AF:

0.264

AC:

39907

AN:

151010

Hom.:

5389

Cov.:

AF XY:

0.261

AC XY:

19266

AN XY:

73774

show subpopulations

African (AFR)

AF:

0.243

AC:

9988

AN:

41048

American (AMR)

AF:

0.260

AC:

3924

AN:

15064

Ashkenazi Jewish (ASJ)

AF:

0.226

AC:

783

AN:

3458

East Asian (EAS)

AF:

0.0909

AC:

471

AN:

5180

South Asian (SAS)

AF:

0.301

AC:

1435

AN:

4768

European-Finnish (FIN)

AF:

0.284

AC:

2958

AN:

10398

Middle Eastern (MID)

AF:

0.229

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.289

AC:

19580

AN:

67802

Other (OTH)

AF:

0.259

AC:

541

AN:

2090

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1422

2844

4267

5689

7111

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.282

Hom.:

10509

Bravo

AF:

0.261

Asia WGS

AF:

0.208

AC:

726

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

1.5

(source)

DANN

Benign

0.87

PhyloP100

-0.23

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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rs17116039

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