Genetic Variant TRA:n.22448054A>G (chr14-22448054-A-G) – 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 0.0948 in 150,356 control chromosomes in the GnomAD database, including 769 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 0.095 ( 769 hom., cov: 25)

Consequence

TRA
intragenic

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.670

Publications

6 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=-0.8).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.153 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
TRA		n.22448054A>G	intragenic_variant
TRD		n.22448054A>G	intragenic_variant
TRD-AS1	NR_148361.1 link	n.225+33187T>C	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+33187T>C		intron_variant	Intron 2 of 2	2

Frequencies

GnomAD3 genomes

AF:

0.0947

AC:

14235

AN:

150238

Hom.:

766

Cov.:

show subpopulations

Gnomad AFR

AF:

0.109

Gnomad AMI

AF:

0.00989

Gnomad AMR

AF:

0.158

Gnomad ASJ

AF:

0.0633

Gnomad EAS

AF:

0.139

Gnomad SAS

AF:

0.0833

Gnomad FIN

AF:

0.0861

Gnomad MID

AF:

0.0506

Gnomad NFE

AF:

0.0739

Gnomad OTH

AF:

0.0996

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

GnomAD4 genome

AF:

0.0948

AC:

14256

AN:

150356

Hom.:

769

Cov.:

AF XY:

0.0962

AC XY:

7062

AN XY:

73408

show subpopulations

African (AFR)

AF:

0.109

AC:

4419

AN:

40662

American (AMR)

AF:

0.159

AC:

2371

AN:

14942

Ashkenazi Jewish (ASJ)

AF:

0.0633

AC:

219

AN:

3460

East Asian (EAS)

AF:

0.139

AC:

715

AN:

5130

South Asian (SAS)

AF:

0.0836

AC:

398

AN:

4762

European-Finnish (FIN)

AF:

0.0861

AC:

895

AN:

10392

Middle Eastern (MID)

AF:

0.0544

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0739

AC:

5002

AN:

67714

Other (OTH)

AF:

0.101

AC:

212

AN:

2090

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

613

1225

1838

2450

3063

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.0846

Hom.:

1856

Bravo

AF:

0.104

Asia WGS

AF:

0.0960

AC:

334

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

6.7

(source)

DANN

Benign

0.73

PhyloP100

0.67

Splicing

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

Publications

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14-22448054-A-G

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