NM_014049.5:c.151-649A>G
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_014049.5(ACAD9):c.151-649A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.393 in 151,996 control chromosomes in the GnomAD database, including 13,564 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 0.39 ( 13564 hom., cov: 32)
Consequence
ACAD9
NM_014049.5 intron
NM_014049.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.134
Publications
5 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]
ACAD9 Gene-Disease associations (from GenCC):
- acyl-CoA dehydrogenase 9 deficiencyInheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: G2P, ClinGen, Orphanet, Labcorp Genetics (formerly Invitae), PanelApp Australia
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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=-0.97).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.612 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.393 AC: 59719AN: 151878Hom.: 13541 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
59719
AN:
151878
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: 0.393 AC: 59792AN: 151996Hom.: 13564 Cov.: 32 AF XY: 0.388 AC XY: 28820AN XY: 74288 show subpopulations
GnomAD4 genome
AF:
AC:
59792
AN:
151996
Hom.:
Cov.:
32
AF XY:
AC XY:
28820
AN XY:
74288
show subpopulations
African (AFR)
AF:
AC:
25620
AN:
41440
American (AMR)
AF:
AC:
5796
AN:
15264
Ashkenazi Jewish (ASJ)
AF:
AC:
1343
AN:
3466
East Asian (EAS)
AF:
AC:
2858
AN:
5154
South Asian (SAS)
AF:
AC:
1308
AN:
4822
European-Finnish (FIN)
AF:
AC:
2505
AN:
10574
Middle Eastern (MID)
AF:
AC:
99
AN:
294
European-Non Finnish (NFE)
AF:
AC:
19238
AN:
67960
Other (OTH)
AF:
AC:
835
AN:
2110
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.506
Heterozygous variant carriers
0
1738
3477
5215
6954
8692
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
540
1080
1620
2160
2700
<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:
1345
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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