Genetic Variant TRA:n.22438076G>A (chr14-22438076-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 0.576 in 149,854 control chromosomes in the GnomAD database, including 25,317 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 0.58 ( 25317 hom., cov: 25)

Consequence

TRA
intragenic

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.461

Publications

2 publications found

Variant links:

Genes affected

TRA (HGNC:12027):

TRA links:

TRD (HGNC:12252):

TRD 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=-0.91).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.682 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
TRA		n.22438076G>A	intragenic_variant
TRD		n.22438076G>A	intragenic_variant
TRD-AS1	NR_148361.1 link	n.225+43165C>T	intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TRD-AS1	ENST00000514473.2 link	n.225+43165C>T		intron_variant	Intron 2 of 2	2

Frequencies

GnomAD3 genomes

AF:

0.576

AC:

86300

AN:

149736

Hom.:

25286

Cov.:

show subpopulations

Gnomad AFR

AF:

0.669

Gnomad AMI

AF:

0.641

Gnomad AMR

AF:

0.439

Gnomad ASJ

AF:

0.589

Gnomad EAS

AF:

0.701

Gnomad SAS

AF:

0.680

Gnomad FIN

AF:

0.544

Gnomad MID

AF:

0.532

Gnomad NFE

AF:

0.539

Gnomad OTH

AF:

0.534

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

GnomAD4 genome

AF:

0.576

AC:

86384

AN:

149854

Hom.:

25317

Cov.:

AF XY:

0.578

AC XY:

42255

AN XY:

73120

show subpopulations

African (AFR)

AF:

0.669

AC:

27166

AN:

40590

American (AMR)

AF:

0.439

AC:

6527

AN:

14876

Ashkenazi Jewish (ASJ)

AF:

0.589

AC:

2031

AN:

3446

East Asian (EAS)

AF:

0.701

AC:

3602

AN:

5140

South Asian (SAS)

AF:

0.680

AC:

3237

AN:

4762

European-Finnish (FIN)

AF:

0.544

AC:

5530

AN:

10172

Middle Eastern (MID)

AF:

0.517

AC:

152

AN:

294

European-Non Finnish (NFE)

AF:

0.539

AC:

36446

AN:

67596

Other (OTH)

AF:

0.537

AC:

1117

AN:

2080

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

1716

3431

5147

6862

8578

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.554

Hom.:

17382

Bravo

AF:

0.565

Asia WGS

AF:

0.694

AC:

2407

AN:

3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

2.1

(source)

DANN

Benign

0.23

PhyloP100

0.46

Splicing

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

Publications

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chr14-22438076-G-A

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