GeneBe

chr14-22370225-A-G

Variant names:

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 0.243 in 150,318 control chromosomes in the GnomAD database, including 4,632 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 0.24 ( 4632 hom., cov: 24)

Consequence

TRA
intragenic

Scores

1

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.557

Publications

5 publications found
Variant links:
Genes affected
TRD-AS1 (HGNC:56197): (TRD antisense RNA 1)

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=-0.91).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.281 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
TRA n.22370225A>G intragenic_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
TRD-AS1ENST00000656379.1 linkn.270+30819T>C intron_variant Intron 3 of 3

Frequencies

GnomAD3 genomes
AF:
0.243
AC:
36524
AN:
150200
Hom.:
4631
Cov.:
24
show subpopulations
Gnomad AFR
AF:
0.242
Gnomad AMI
AF:
0.201
Gnomad AMR
AF:
0.174
Gnomad ASJ
AF:
0.168
Gnomad EAS
AF:
0.0800
Gnomad SAS
AF:
0.136
Gnomad FIN
AF:
0.241
Gnomad MID
AF:
0.203
Gnomad NFE
AF:
0.284
Gnomad OTH
AF:
0.233
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.243
AC:
36555
AN:
150318
Hom.:
4632
Cov.:
24
AF XY:
0.237
AC XY:
17408
AN XY:
73394
show subpopulations
African (AFR)
AF:
0.243
AC:
9901
AN:
40772
American (AMR)
AF:
0.174
AC:
2596
AN:
14962
Ashkenazi Jewish (ASJ)
AF:
0.168
AC:
579
AN:
3452
East Asian (EAS)
AF:
0.0798
AC:
409
AN:
5128
South Asian (SAS)
AF:
0.136
AC:
647
AN:
4760
European-Finnish (FIN)
AF:
0.241
AC:
2493
AN:
10330
Middle Eastern (MID)
AF:
0.197
AC:
58
AN:
294
European-Non Finnish (NFE)
AF:
0.284
AC:
19209
AN:
67622
Other (OTH)
AF:
0.230
AC:
480
AN:
2086
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.501
Heterozygous variant carriers
0
1287
2574
3862
5149
6436
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
370
740
1110
1480
1850
<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:
0.260
Hom.:
9178
Bravo
AF:
0.238

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
4.4
PhyloP100
0.56

Splicing

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

Publications

Other links and lift over

dbSNP: rs8014927; hg19: chr14-22838630; API