19-15898482-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 0.296 in 151,670 control chromosomes in the GnomAD database, including 7,082 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 0.30 ( 7082 hom., cov: 29)
Consequence
Unknown
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.347
Publications
5 publications found
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ACMG classification
Our verdict: Benign. The variant received -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.347 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|
Frequencies
GnomAD3 genomes AF: 0.296 AC: 44827AN: 151552Hom.: 7087 Cov.: 29 show subpopulations
GnomAD3 genomes
AF:
AC:
44827
AN:
151552
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 AF: 0.296 AC: 44821AN: 151670Hom.: 7082 Cov.: 29 AF XY: 0.294 AC XY: 21799AN XY: 74112 show subpopulations
GnomAD4 genome
AF:
AC:
44821
AN:
151670
Hom.:
Cov.:
29
AF XY:
AC XY:
21799
AN XY:
74112
show subpopulations
African (AFR)
AF:
AC:
7905
AN:
41342
American (AMR)
AF:
AC:
4710
AN:
15252
Ashkenazi Jewish (ASJ)
AF:
AC:
906
AN:
3466
East Asian (EAS)
AF:
AC:
1194
AN:
5144
South Asian (SAS)
AF:
AC:
1315
AN:
4798
European-Finnish (FIN)
AF:
AC:
3944
AN:
10498
Middle Eastern (MID)
AF:
AC:
48
AN:
292
European-Non Finnish (NFE)
AF:
AC:
23826
AN:
67858
Other (OTH)
AF:
AC:
583
AN:
2110
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.519
Heterozygous variant carriers
0
1543
3085
4628
6170
7713
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
448
896
1344
1792
2240
<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.:
Bravo
AF:
Asia WGS
AF:
AC:
818
AN:
3478
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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