Genetic Variant TRA:n.22303409T>C (chr14-22303409-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 variant allele was found at a frequency of 0.848 in 151,122 control chromosomes in the GnomAD database, including 54,733 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 0.85 ( 54733 hom., cov: 25)

Consequence

TRA
intragenic

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.347

Publications

4 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 (Cadd=4.289).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.94 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRA		n.22303409T>C		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TRD-AS1	ENST00000656379.1 link	n.270+97635A>G		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes

AF:

0.848

AC:

128075

AN:

151004

Hom.:

54681

Cov.:

show subpopulations

Gnomad AFR

AF:

0.948

Gnomad AMI

AF:

0.604

Gnomad AMR

AF:

0.858

Gnomad ASJ

AF:

0.778

Gnomad EAS

AF:

0.891

Gnomad SAS

AF:

0.822

Gnomad FIN

AF:

0.836

Gnomad MID

AF:

0.826

Gnomad NFE

AF:

0.793

Gnomad OTH

AF:

0.845

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

GnomAD4 genome

AF:

0.848

AC:

128184

AN:

151122

Hom.:

54733

Cov.:

AF XY:

0.851

AC XY:

62850

AN XY:

73876

show subpopulations

African (AFR)

AF:

0.948

AC:

38936

AN:

41060

American (AMR)

AF:

0.858

AC:

12936

AN:

15084

Ashkenazi Jewish (ASJ)

AF:

0.778

AC:

2688

AN:

3454

East Asian (EAS)

AF:

0.891

AC:

4610

AN:

5172

South Asian (SAS)

AF:

0.820

AC:

3907

AN:

4764

European-Finnish (FIN)

AF:

0.836

AC:

8754

AN:

10468

Middle Eastern (MID)

AF:

0.823

AC:

242

AN:

294

European-Non Finnish (NFE)

AF:

0.793

AC:

53777

AN:

67810

Other (OTH)

AF:

0.847

AC:

1784

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

914

1828

2741

3655

4569

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.807

Hom.:

63973

Bravo

AF:

0.854

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

CADD

Benign

4.3

(source)

PhyloP100

-0.35

Splicing

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

Publications

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14-22303409-T-C

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