dbSNP rs4982599: TRA:n.22279581G>A (chr14-22279581-G-A) – 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 0.325 in 150,012 control chromosomes in the GnomAD database, including 8,922 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 0.33 ( 8922 hom., cov: 25)

Consequence

TRA
intragenic

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.290

Publications

3 publications found

Variant links:

Genes affected

TRA (HGNC:12027):

TRA links:

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

TRD-AS1 links:

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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=-0.95).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.492 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRA		n.22279581G>A		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TRD-AS1	ENST00000656379.1 link	n.271-78199C>T		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes

AF:

0.325

AC:

48661

AN:

149894

Hom.:

8886

Cov.:

show subpopulations

Gnomad AFR

AF:

0.497

Gnomad AMI

AF:

0.172

Gnomad AMR

AF:

0.261

Gnomad ASJ

AF:

0.348

Gnomad EAS

AF:

0.458

Gnomad SAS

AF:

0.353

Gnomad FIN

AF:

0.212

Gnomad MID

AF:

0.274

Gnomad NFE

AF:

0.242

Gnomad OTH

AF:

0.318

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

GnomAD4 genome

AF:

0.325

AC:

48761

AN:

150012

Hom.:

8922

Cov.:

AF XY:

0.323

AC XY:

23619

AN XY:

73172

show subpopulations

African (AFR)

AF:

0.498

AC:

20182

AN:

40536

American (AMR)

AF:

0.262

AC:

3916

AN:

14958

Ashkenazi Jewish (ASJ)

AF:

0.348

AC:

1203

AN:

3456

East Asian (EAS)

AF:

0.458

AC:

2328

AN:

5078

South Asian (SAS)

AF:

0.353

AC:

1667

AN:

4720

European-Finnish (FIN)

AF:

0.212

AC:

2198

AN:

10386

Middle Eastern (MID)

AF:

0.281

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.242

AC:

16355

AN:

67592

Other (OTH)

AF:

0.323

AC:

675

AN:

2092

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1467

2934

4402

5869

7336

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.279

Hom.:

3295

Bravo

AF:

0.337

Asia WGS

AF:

0.418

AC:

1454

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

5.0

(source)

DANN

Benign

0.71

PhyloP100

0.29

Splicing

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

Publications

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rs4982599

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