NM_014049.5:c.1569_1571dupCAT
Variant summary
Our verdict is Uncertain significance. The variant received 5 ACMG points: 5P and 0B. PM1PM2PM4_Supporting
The NM_014049.5(ACAD9):c.1569_1571dupCAT(p.Ile523dup) variant causes a disruptive inframe insertion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000558 in 1,613,366 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★★).
Frequency
Genomes: 𝑓 0.000013 ( 0 hom., cov: 33)
Exomes 𝑓: 0.0000048 ( 0 hom. )
Consequence
ACAD9
NM_014049.5 disruptive_inframe_insertion
NM_014049.5 disruptive_inframe_insertion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -0.564
Publications
0 publications found
Genes affected
ACAD9 (HGNC:21497): (acyl-CoA dehydrogenase family member 9) This gene encodes a member of the acyl-CoA dehydrogenase family. Members of this family of proteins localize to the mitochondria and catalyze the rate-limiting step in the beta-oxidation of fatty acyl-CoA. The encoded protein is specifically active toward palmitoyl-CoA and long-chain unsaturated substrates. Mutations in this gene cause acyl-CoA dehydrogenase family member type 9 deficiency. Alternate splicing results in multiple transcript variants.[provided by RefSeq, Mar 2010]
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ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 5 ACMG points.
PM1
In a hotspot region, there are 5 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 0 benign, 4 uncertain in NM_014049.5
PM2
Very rare variant in population databases, with high coverage;
PM4
Nonframeshift variant in NON repetitive region in NM_014049.5. Strenght limited to Supporting due to length of the change: 1aa.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_014049.5. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| ACAD9 | NM_014049.5 | MANE Select | c.1569_1571dupCAT | p.Ile523dup | disruptive_inframe_insertion | Exon 16 of 18 | NP_054768.2 | ||
| CFAP92 | NM_001394090.1 | MANE Select | c.*274_*276dupATG | 3_prime_UTR | Exon 16 of 16 | NP_001381019.1 | A0A2R8YFM9 | ||
| ACAD9 | NM_001410805.1 | c.1200_1202dupCAT | p.Ile400dup | disruptive_inframe_insertion | Exon 15 of 17 | NP_001397734.1 | Q9H9W4 |
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| ACAD9 | ENST00000308982.12 | TSL:1 MANE Select | c.1569_1571dupCAT | p.Ile523dup | disruptive_inframe_insertion | Exon 16 of 18 | ENSP00000312618.7 | Q9H845 | |
| CFAP92 | ENST00000645291.3 | MANE Select | c.*274_*276dupATG | 3_prime_UTR | Exon 16 of 16 | ENSP00000496592.2 | A0A2R8YFM9 | ||
| ACAD9 | ENST00000511526.5 | TSL:1 | n.1102_1104dupCAT | non_coding_transcript_exon | Exon 12 of 14 |
Frequencies
GnomAD3 genomes 0.0000131 AC: 2AN: 152228Hom.: 0 Cov.: 33 show subpopulations
GnomAD3 genomes
AF:
AC:
2
AN:
152228
Hom.:
Cov.:
33
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: 0.00000479 AC: 7AN: 1461138Hom.: 0 Cov.: 32 AF XY: 0.00000275 AC XY: 2AN XY: 726790 show subpopulations
GnomAD4 exome
AF:
AC:
7
AN:
1461138
Hom.:
Cov.:
32
AF XY:
AC XY:
2
AN XY:
726790
show subpopulations
African (AFR)
AF:
AC:
0
AN:
33478
American (AMR)
AF:
AC:
0
AN:
44672
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
25988
East Asian (EAS)
AF:
AC:
0
AN:
39694
South Asian (SAS)
AF:
AC:
0
AN:
85940
European-Finnish (FIN)
AF:
AC:
0
AN:
53394
Middle Eastern (MID)
AF:
AC:
0
AN:
5766
European-Non Finnish (NFE)
AF:
AC:
0
AN:
1111852
Other (OTH)
AF:
AC:
7
AN:
60354
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.439
Heterozygous variant carriers
0
1
2
2
3
4
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome 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
GnomAD4 genome 0.0000131 AC: 2AN: 152228Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74384 show subpopulations
GnomAD4 genome
AF:
AC:
2
AN:
152228
Hom.:
Cov.:
33
AF XY:
AC XY:
0
AN XY:
74384
show subpopulations
African (AFR)
AF:
AC:
2
AN:
41456
American (AMR)
AF:
AC:
0
AN:
15284
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3472
East Asian (EAS)
AF:
AC:
0
AN:
5192
South Asian (SAS)
AF:
AC:
0
AN:
4834
European-Finnish (FIN)
AF:
AC:
0
AN:
10626
Middle Eastern (MID)
AF:
AC:
0
AN:
316
European-Non Finnish (NFE)
AF:
AC:
0
AN:
68044
Other (OTH)
AF:
AC:
0
AN:
2092
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.500
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
2
AN:
3478
ClinVar
ClinVar submissions
View on ClinVar Significance:Uncertain significance
Revision:criteria provided, multiple submitters, no conflicts
Pathogenic
VUS
Benign
Condition
-
1
-
Acyl-CoA dehydrogenase 9 deficiency (1)
-
1
-
not provided (1)
Computational 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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