20-30393452-C-T
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The NR_003579.2(FRG1BP):n.568-99C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.080 ( 0 hom., cov: 28)
Exomes 𝑓: 0.00045 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
FRG1BP
NR_003579.2 intron
NR_003579.2 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.384
Publications
2 publications found
Genes affected
FRG1BP (HGNC:15792): (FSHD region gene 1 family member B, pseudogene)
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -6 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.99).
BP6
Variant 20-30393452-C-T is Benign according to our data. Variant chr20-30393452-C-T is described in ClinVar as Benign. ClinVar VariationId is 982083.Status of the report is criteria_provided_single_submitter, 1 stars.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NR_003579.2. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| FRG1BP | NR_003579.2 | n.568-99C>T | intron | N/A | |||||
| FRG1BP | NR_145491.1 | n.568-99C>T | intron | N/A |
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| FRG1BP | ENST00000278882.8 | TSL:6 | n.418-99C>T | intron | N/A | ||||
| FRG1BP | ENST00000829738.1 | n.854-99C>T | intron | N/A | |||||
| FRG1BP | ENST00000829739.1 | n.878-99C>T | intron | N/A |
Frequencies
GnomAD3 genomes 0.0795 AC: 3406AN: 42848Hom.: 0 Cov.: 28 show subpopulations
GnomAD3 genomes
AF:
AC:
3406
AN:
42848
Hom.:
Cov.:
28
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:
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.000452 AC: 527AN: 1166380Hom.: 0 AF XY: 0.000411 AC XY: 235AN XY: 571650 show subpopulations ⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
AF:
AC:
527
AN:
1166380
Hom.:
AF XY:
AC XY:
235
AN XY:
571650
show subpopulations
⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
AC:
17
AN:
24710
American (AMR)
AF:
AC:
16
AN:
21716
Ashkenazi Jewish (ASJ)
AF:
AC:
26
AN:
18350
East Asian (EAS)
AF:
AC:
36
AN:
28500
South Asian (SAS)
AF:
AC:
38
AN:
56784
European-Finnish (FIN)
AF:
AC:
37
AN:
40142
Middle Eastern (MID)
AF:
AC:
6
AN:
4814
European-Non Finnish (NFE)
AF:
AC:
310
AN:
924450
Other (OTH)
AF:
AC:
41
AN:
46914
⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.239
Heterozygous variant carriers
0
89
177
266
354
443
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
0
4
8
12
16
20
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome 0.0796 AC: 3415AN: 42910Hom.: 0 Cov.: 28 AF XY: 0.0796 AC XY: 1705AN XY: 21432 show subpopulations ⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.
GnomAD4 genome
Data not reliable, filtered out with message: AS_VQSR;InbreedingCoeff
AF:
AC:
3415
AN:
42910
Hom.:
Cov.:
28
AF XY:
AC XY:
1705
AN XY:
21432
show subpopulations
⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
AC:
1286
AN:
11602
American (AMR)
AF:
AC:
453
AN:
4394
Ashkenazi Jewish (ASJ)
AF:
AC:
69
AN:
906
East Asian (EAS)
AF:
AC:
107
AN:
1522
South Asian (SAS)
AF:
AC:
117
AN:
1400
European-Finnish (FIN)
AF:
AC:
243
AN:
3620
Middle Eastern (MID)
AF:
AC:
12
AN:
90
European-Non Finnish (NFE)
AF:
AC:
1063
AN:
18522
Other (OTH)
AF:
AC:
52
AN:
680
⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.244
Heterozygous variant carriers
0
529
1059
1588
2118
2647
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Variant carriers
0
34
68
102
136
170
<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:
Hom.:
ClinVar
ClinVar submissions
View on ClinVar Significance:Benign
Revision:criteria provided, single submitter
Pathogenic
VUS
Benign
Condition
-
-
1
not specified (1)
Computational 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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