12-20345102-A-T
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong
The variant allele was found at a frequency of 0.0000275 in 145,710 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.000027 ( 0 hom., cov: 29)
Consequence
Unknown
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -4.36
Publications
25 publications found
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ACMG classification
Our verdict: Likely_benign. The variant received -2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-1.07).
Variant Effect in Transcripts
RefSeq Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
There are no transcript annotations for this variant. | |||||||||
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
There are no transcript annotations for this variant. | |||||||||
Frequencies
GnomAD3 genomes 0.0000275 AC: 4AN: 145588Hom.: 0 Cov.: 29 show subpopulations
GnomAD3 genomes
AF:
AC:
4
AN:
145588
Hom.:
Cov.:
29
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 0.0000275 AC: 4AN: 145710Hom.: 0 Cov.: 29 AF XY: 0.0000421 AC XY: 3AN XY: 71250 show subpopulations
GnomAD4 genome
AF:
AC:
4
AN:
145710
Hom.:
Cov.:
29
AF XY:
AC XY:
3
AN XY:
71250
show subpopulations
African (AFR)
AF:
AC:
1
AN:
39126
American (AMR)
AF:
AC:
0
AN:
14820
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3324
East Asian (EAS)
AF:
AC:
0
AN:
4682
South Asian (SAS)
AF:
AC:
1
AN:
4470
European-Finnish (FIN)
AF:
AC:
0
AN:
10342
Middle Eastern (MID)
AF:
AC:
1
AN:
284
European-Non Finnish (NFE)
AF:
AC:
1
AN:
65744
Other (OTH)
AF:
AC:
0
AN:
2024
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.538
Heterozygous variant carriers
0
1
1
2
2
3
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Variant carriers
0
2
4
6
8
10
<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
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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