NM_001646.3:c.77-785G>A
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The NM_001646.3(APOC4):c.77-785G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0131 in 152,300 control chromosomes in the GnomAD database, including 21 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 0.013 ( 21 hom., cov: 31)
Consequence
APOC4
NM_001646.3 intron
NM_001646.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -2.52
Publications
19 publications found
Genes affected
APOC4 (HGNC:611): (apolipoprotein C4) This gene encodes a lipid-binding protein belonging to the apolipoprotein gene family. The protein is thought to play a role in lipid metabolism. Polymorphisms in this gene may influence circulating lipid levels and may be associated with coronary artery disease risk. This gene is present in a cluster with other related apolipoprotein genes on chromosome 19. Naturally occurring read-through transcription exists between this gene and the neighboring downstream apolipoprotein C-II (APOC2) gene. [provided by RefSeq, Mar 2011]
APOC4-APOC2 (HGNC:44426): (APOC4-APOC2 readthrough (NMD candidate)) This locus represents naturally occurring read-through transcription between the neighboring apolipoprotein C-IV (APOC4) and apolipoprotein C-II (APOC2) genes on chromosome 19. The read-through transcript is a candidate for nonsense-mediated mRNA decay (NMD), and is thus unlikely to produce a protein product. [provided by RefSeq, Mar 2011]
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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=-0.95).
BS1
Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0131 (1994/152300) while in subpopulation NFE AF = 0.0223 (1514/68026). AF 95% confidence interval is 0.0213. There are 21 homozygotes in GnomAd4. There are 880 alleles in the male GnomAd4 subpopulation. Median coverage is 31. This position passed quality control check.
BS2
High Homozygotes in GnomAd4 at 21 gene
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
APOC4 | ENST00000592954.2 | c.77-785G>A | intron_variant | Intron 1 of 2 | 1 | NM_001646.3 | ENSP00000468236.1 | |||
APOC4-APOC2 | ENST00000589057.5 | c.77-785G>A | intron_variant | Intron 1 of 4 | 5 | ENSP00000468139.1 | ||||
APOC4 | ENST00000591600.1 | c.77-785G>A | intron_variant | Intron 1 of 1 | 3 | ENSP00000466444.1 | ||||
APOC4-APOC2 | ENST00000585685.5 | n.77-785G>A | intron_variant | Intron 1 of 5 | 5 | ENSP00000467185.1 |
Frequencies
GnomAD3 genomes AF: 0.0131 AC: 1996AN: 152182Hom.: 21 Cov.: 31 show subpopulations
GnomAD3 genomes
AF:
AC:
1996
AN:
152182
Hom.:
Cov.:
31
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: 0.0131 AC: 1994AN: 152300Hom.: 21 Cov.: 31 AF XY: 0.0118 AC XY: 880AN XY: 74468 show subpopulations
GnomAD4 genome
AF:
AC:
1994
AN:
152300
Hom.:
Cov.:
31
AF XY:
AC XY:
880
AN XY:
74468
show subpopulations
African (AFR)
AF:
AC:
164
AN:
41574
American (AMR)
AF:
AC:
49
AN:
15282
Ashkenazi Jewish (ASJ)
AF:
AC:
75
AN:
3468
East Asian (EAS)
AF:
AC:
0
AN:
5176
South Asian (SAS)
AF:
AC:
6
AN:
4832
European-Finnish (FIN)
AF:
AC:
142
AN:
10622
Middle Eastern (MID)
AF:
AC:
0
AN:
294
European-Non Finnish (NFE)
AF:
AC:
1514
AN:
68026
Other (OTH)
AF:
AC:
15
AN:
2114
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.499
Heterozygous variant carriers
0
102
205
307
410
512
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
22
44
66
88
110
<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:
4
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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