chr14-22284990-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 0.264 in 151,010 control chromosomes in the GnomAD database, including 5,389 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 0.26 ( 5389 hom., cov: 26)
Consequence
TRA
intragenic
intragenic
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.225
Publications
5 publications found
Genes affected
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=-0.89).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.288 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TRA | n.22284990A>G | intragenic_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TRD-AS1 | ENST00000656379.1 | n.271-83608T>C | intron_variant | Intron 3 of 3 |
Frequencies
GnomAD3 genomes AF: 0.264 AC: 39855AN: 150892Hom.: 5379 Cov.: 26 show subpopulations
GnomAD3 genomes
AF:
AC:
39855
AN:
150892
Hom.:
Cov.:
26
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.264 AC: 39907AN: 151010Hom.: 5389 Cov.: 26 AF XY: 0.261 AC XY: 19266AN XY: 73774 show subpopulations
GnomAD4 genome
AF:
AC:
39907
AN:
151010
Hom.:
Cov.:
26
AF XY:
AC XY:
19266
AN XY:
73774
show subpopulations
African (AFR)
AF:
AC:
9988
AN:
41048
American (AMR)
AF:
AC:
3924
AN:
15064
Ashkenazi Jewish (ASJ)
AF:
AC:
783
AN:
3458
East Asian (EAS)
AF:
AC:
471
AN:
5180
South Asian (SAS)
AF:
AC:
1435
AN:
4768
European-Finnish (FIN)
AF:
AC:
2958
AN:
10398
Middle Eastern (MID)
AF:
AC:
67
AN:
292
European-Non Finnish (NFE)
AF:
AC:
19580
AN:
67802
Other (OTH)
AF:
AC:
541
AN:
2090
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.504
Heterozygous variant carriers
0
1422
2844
4267
5689
7111
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
726
AN:
3476
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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