Genetic Variant TRA:n.22446824G>T (chr14-22446824-G-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 0.133 in 150,182 control chromosomes in the GnomAD database, including 1,796 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 0.13 ( 1796 hom., cov: 25)

Consequence

TRA
intragenic

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.869

Publications

5 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=-0.86).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.448 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
TRA		n.22446824G>T	intragenic_variant
TRD		n.22446824G>T	intragenic_variant
TRD-AS1	NR_148361.1 link	n.225+34417C>A	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+34417C>A		intron_variant	Intron 2 of 2	2

Frequencies

GnomAD3 genomes

AF:

0.134

AC:

20053

AN:

150064

Hom.:

1801

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0837

Gnomad AMI

AF:

0.191

Gnomad AMR

AF:

0.145

Gnomad ASJ

AF:

0.153

Gnomad EAS

AF:

0.464

Gnomad SAS

AF:

0.251

Gnomad FIN

AF:

0.162

Gnomad MID

AF:

0.161

Gnomad NFE

AF:

0.122

Gnomad OTH

AF:

0.119

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

GnomAD4 genome

AF:

0.133

AC:

20040

AN:

150182

Hom.:

1796

Cov.:

AF XY:

0.139

AC XY:

10219

AN XY:

73320

show subpopulations

African (AFR)

AF:

0.0835

AC:

3396

AN:

40664

American (AMR)

AF:

0.145

AC:

2160

AN:

14890

Ashkenazi Jewish (ASJ)

AF:

0.153

AC:

529

AN:

3460

East Asian (EAS)

AF:

0.464

AC:

2371

AN:

5112

South Asian (SAS)

AF:

0.250

AC:

1190

AN:

4754

European-Finnish (FIN)

AF:

0.162

AC:

1673

AN:

10332

Middle Eastern (MID)

AF:

0.150

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.122

AC:

8257

AN:

67680

Other (OTH)

AF:

0.118

AC:

248

AN:

2094

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

801

1602

2404

3205

4006

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.127

Hom.:

4264

Bravo

AF:

0.126

Asia WGS

AF:

0.334

AC:

1163

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

4.5

(source)

DANN

Benign

0.50

PhyloP100

0.87

Splicing

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

Publications

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14-22446824-G-T

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