Genetic Variant TRA:n.22323783T>C (chr14-22323783-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 0.528 in 150,674 control chromosomes in the GnomAD database, including 21,146 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 0.53 ( 21146 hom., cov: 26)

Consequence

TRA
intragenic

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0450

Publications

2 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 (BayesDel_noAF=-0.91).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.665 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRA		n.22323783T>C		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TRD-AS1	ENST00000656379.1 link	n.270+77261A>G		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes

AF:

0.528

AC:

79447

AN:

150556

Hom.:

21129

Cov.:

show subpopulations

Gnomad AFR

AF:

0.587

Gnomad AMI

AF:

0.466

Gnomad AMR

AF:

0.528

Gnomad ASJ

AF:

0.479

Gnomad EAS

AF:

0.684

Gnomad SAS

AF:

0.642

Gnomad FIN

AF:

0.534

Gnomad MID

AF:

0.414

Gnomad NFE

AF:

0.476

Gnomad OTH

AF:

0.516

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

GnomAD4 genome

AF:

0.528

AC:

79507

AN:

150674

Hom.:

21146

Cov.:

AF XY:

0.531

AC XY:

39064

AN XY:

73576

show subpopulations

African (AFR)

AF:

0.586

AC:

23963

AN:

40894

American (AMR)

AF:

0.528

AC:

7934

AN:

15030

Ashkenazi Jewish (ASJ)

AF:

0.479

AC:

1650

AN:

3448

East Asian (EAS)

AF:

0.684

AC:

3526

AN:

5158

South Asian (SAS)

AF:

0.642

AC:

3048

AN:

4750

European-Finnish (FIN)

AF:

0.534

AC:

5540

AN:

10384

Middle Eastern (MID)

AF:

0.418

AC:

122

AN:

292

European-Non Finnish (NFE)

AF:

0.476

AC:

32212

AN:

67716

Other (OTH)

AF:

0.520

AC:

1089

AN:

2094

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1796

3592

5387

7183

8979

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.496

Hom.:

33286

Bravo

AF:

0.531

Asia WGS

AF:

0.651

AC:

2262

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

6.2

(source)

DANN

Benign

0.80

PhyloP100

0.045

Splicing

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

Publications

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chr14-22323783-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