NM_006111.3:c.883+677A>C
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_006111.3(ACAA2):c.883+677A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.6 in 151,976 control chromosomes in the GnomAD database, including 27,435 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 0.60 ( 27435 hom., cov: 32)
Consequence
ACAA2
NM_006111.3 intron
NM_006111.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.163
Publications
4 publications found
Genes affected
ACAA2 (HGNC:83): (acetyl-CoA acyltransferase 2) The encoded protein catalyzes the last step of the mitochondrial fatty acid beta-oxidation spiral. Unlike most mitochondrial matrix proteins, it contains a non-cleavable amino-terminal targeting signal. [provided by RefSeq, Jul 2008]
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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).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.634 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ACAA2 | ENST00000285093.15 | c.883+677A>C | intron_variant | Intron 7 of 9 | 1 | NM_006111.3 | ENSP00000285093.8 | |||
ACAA2 | ENST00000587994.5 | c.874+677A>C | intron_variant | Intron 7 of 9 | 5 | ENSP00000466015.1 | ||||
ACAA2 | ENST00000589432.5 | c.718+677A>C | intron_variant | Intron 7 of 9 | 5 | ENSP00000466466.1 |
Frequencies
GnomAD3 genomes AF: 0.600 AC: 91061AN: 151860Hom.: 27419 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
91061
AN:
151860
Hom.:
Cov.:
32
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: 0.600 AC: 91130AN: 151976Hom.: 27435 Cov.: 32 AF XY: 0.599 AC XY: 44519AN XY: 74290 show subpopulations
GnomAD4 genome
AF:
AC:
91130
AN:
151976
Hom.:
Cov.:
32
AF XY:
AC XY:
44519
AN XY:
74290
show subpopulations
African (AFR)
AF:
AC:
25019
AN:
41432
American (AMR)
AF:
AC:
9845
AN:
15282
Ashkenazi Jewish (ASJ)
AF:
AC:
2396
AN:
3468
East Asian (EAS)
AF:
AC:
2843
AN:
5172
South Asian (SAS)
AF:
AC:
2816
AN:
4814
European-Finnish (FIN)
AF:
AC:
5582
AN:
10560
Middle Eastern (MID)
AF:
AC:
223
AN:
292
European-Non Finnish (NFE)
AF:
AC:
40403
AN:
67932
Other (OTH)
AF:
AC:
1351
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.504
Heterozygous variant carriers
0
1914
3827
5741
7654
9568
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
758
1516
2274
3032
3790
<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:
2056
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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