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:

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=-0.86).

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

chr14-22446824-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