chr22-36191797-ACT-A
Variant names:
Variant summary
Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1
The NM_001386885.1(APOL4):c.323_324delAG(p.Glu108ValfsTer21) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.478 in 1,613,480 control chromosomes in the GnomAD database, including 190,083 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.40 ( 13527 hom., cov: 0)
Exomes 𝑓: 0.49 ( 176556 hom. )
Consequence
APOL4
NM_001386885.1 frameshift
NM_001386885.1 frameshift
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.263
Publications
10 publications found
Genes affected
APOL4 (HGNC:14867): (apolipoprotein L4) This gene encodes a member of the apolipoprotein L family. The encoded protein may play a role in lipid exchange and transport throughout the body, as well as in reverse cholesterol transport from peripheral cells to the liver. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Sep 2020]
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ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -8 ACMG points.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.503 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
APOL4 | NM_001386885.1 | c.323_324delAG | p.Glu108ValfsTer21 | frameshift_variant | Exon 4 of 4 | ENST00000683024.1 | NP_001373814.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.404 AC: 61239AN: 151702Hom.: 13508 Cov.: 0 show subpopulations
GnomAD3 genomes
AF:
AC:
61239
AN:
151702
Hom.:
Cov.:
0
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 AF: 0.485 AC: 709449AN: 1461658Hom.: 176556 AF XY: 0.485 AC XY: 352983AN XY: 727112 show subpopulations
GnomAD4 exome
AF:
AC:
709449
AN:
1461658
Hom.:
AF XY:
AC XY:
352983
AN XY:
727112
show subpopulations
African (AFR)
AF:
AC:
7500
AN:
33480
American (AMR)
AF:
AC:
19847
AN:
44722
Ashkenazi Jewish (ASJ)
AF:
AC:
13290
AN:
26136
East Asian (EAS)
AF:
AC:
7308
AN:
39698
South Asian (SAS)
AF:
AC:
38687
AN:
86258
European-Finnish (FIN)
AF:
AC:
23912
AN:
53366
Middle Eastern (MID)
AF:
AC:
2978
AN:
5768
European-Non Finnish (NFE)
AF:
AC:
567559
AN:
1111858
Other (OTH)
AF:
AC:
28368
AN:
60372
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.532
Heterozygous variant carriers
0
23922
47844
71766
95688
119610
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Exome Hom
Variant carriers
0
16212
32424
48636
64848
81060
<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 AF: 0.404 AC: 61298AN: 151822Hom.: 13527 Cov.: 0 AF XY: 0.400 AC XY: 29667AN XY: 74198 show subpopulations
GnomAD4 genome
AF:
AC:
61298
AN:
151822
Hom.:
Cov.:
0
AF XY:
AC XY:
29667
AN XY:
74198
show subpopulations
African (AFR)
AF:
AC:
9636
AN:
41394
American (AMR)
AF:
AC:
6375
AN:
15266
Ashkenazi Jewish (ASJ)
AF:
AC:
1777
AN:
3464
East Asian (EAS)
AF:
AC:
934
AN:
5144
South Asian (SAS)
AF:
AC:
2057
AN:
4814
European-Finnish (FIN)
AF:
AC:
4670
AN:
10536
Middle Eastern (MID)
AF:
AC:
147
AN:
294
European-Non Finnish (NFE)
AF:
AC:
34454
AN:
67906
Other (OTH)
AF:
AC:
916
AN:
2104
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.499
Heterozygous variant carriers
0
1790
3580
5369
7159
8949
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
600
1200
1800
2400
3000
<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:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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