Genetic Variant TRA:n.21853868G>T (chr14-21853868-G-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B.

-12

BP4_StrongBA1

The variant allele was found at a frequency of 0.433 in 151,842 control chromosomes in the GnomAD database, including 14,776 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 0.43 ( 14776 hom., cov: 31)

Consequence

TRA
intragenic

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0540

Publications

1 publications found

Variant links:

Genes affected

TRA (HGNC:12027):

TRA 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=-0.88).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.526 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRA		n.21853868G>T		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes

AF:

0.433

AC:

65703

AN:

151724

Hom.:

14775

Cov.:

show subpopulations

Gnomad AFR

AF:

0.512

Gnomad AMI

AF:

0.282

Gnomad AMR

AF:

0.535

Gnomad ASJ

AF:

0.405

Gnomad EAS

AF:

0.370

Gnomad SAS

AF:

0.461

Gnomad FIN

AF:

0.268

Gnomad MID

AF:

0.516

Gnomad NFE

AF:

0.393

Gnomad OTH

AF:

0.433

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

GnomAD4 genome

AF:

0.433

AC:

65734

AN:

151842

Hom.:

14776

Cov.:

AF XY:

0.428

AC XY:

31726

AN XY:

74162

show subpopulations

African (AFR)

AF:

0.512

AC:

21168

AN:

41370

American (AMR)

AF:

0.536

AC:

8190

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.405

AC:

1406

AN:

3472

East Asian (EAS)

AF:

0.370

AC:

1909

AN:

5166

South Asian (SAS)

AF:

0.461

AC:

2214

AN:

4806

European-Finnish (FIN)

AF:

0.268

AC:

2822

AN:

10524

Middle Eastern (MID)

AF:

0.490

AC:

143

AN:

292

European-Non Finnish (NFE)

AF:

0.393

AC:

26724

AN:

67920

Other (OTH)

AF:

0.428

AC:

901

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1858

3715

5573

7430

9288

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

608

1216

1824

2432

3040

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.412

Hom.:

1717

Bravo

AF:

0.457

Asia WGS

AF:

0.346

AC:

1201

AN:

3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

3.8

(source)

DANN

Benign

0.57

PhyloP100

-0.054

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.

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