Genetic Variant TRA:n.22471852C>T (chr14-22471852-C-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 0.122 in 151,460 control chromosomes in the GnomAD database, including 1,318 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 0.12 ( 1318 hom., cov: 26)

Consequence

TRA
intragenic

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.879

Publications

6 publications found

Variant links:

Genes affected

TRA (HGNC:12027):

TRA 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=-0.8).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.171 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRA		n.22471852C>T		intragenic_variant
TRD-AS1	NR_148361.1 link	n.225+9389G>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+9389G>A		intron_variant	Intron 2 of 2	2
TRD-AS1	ENST00000556777.2 link	n.563-6566G>A		intron_variant	Intron 2 of 3	3

Frequencies

GnomAD3 genomes

AF:

0.122

AC:

18427

AN:

151342

Hom.:

1320

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0632

Gnomad AMI

AF:

0.257

Gnomad AMR

AF:

0.104

Gnomad ASJ

AF:

0.134

Gnomad EAS

AF:

0.00193

Gnomad SAS

AF:

0.0784

Gnomad FIN

AF:

0.106

Gnomad MID

AF:

0.104

Gnomad NFE

AF:

0.173

Gnomad OTH

AF:

0.122

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

GnomAD4 genome

AF:

0.122

AC:

18430

AN:

151460

Hom.:

1318

Cov.:

AF XY:

0.118

AC XY:

8710

AN XY:

74046

show subpopulations

African (AFR)

AF:

0.0632

AC:

2606

AN:

41236

American (AMR)

AF:

0.104

AC:

1578

AN:

15158

Ashkenazi Jewish (ASJ)

AF:

0.134

AC:

463

AN:

3466

East Asian (EAS)

AF:

0.00193

AC:

AN:

5178

South Asian (SAS)

AF:

0.0783

AC:

375

AN:

4790

European-Finnish (FIN)

AF:

0.106

AC:

1114

AN:

10504

Middle Eastern (MID)

AF:

0.109

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.173

AC:

11765

AN:

67822

Other (OTH)

AF:

0.120

AC:

253

AN:

2102

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

783

1565

2348

3130

3913

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

212

424

636

848

1060

<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:

0.134

Hom.:

1079

Bravo

AF:

0.120

Asia WGS

AF:

0.0400

AC:

140

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

1.6

(source)

DANN

Benign

0.60

PhyloP100

-0.88

Mutation Taster

=100/0

polymorphism

(source)

Splicing

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

Publications

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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