NM_014049.5:c.22C>T
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_014049.5(ACAD9):c.22C>T(p.Leu8Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: not found (cov: 33)
Exomes 𝑓: 6.8e-7 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
ACAD9
NM_014049.5 synonymous
NM_014049.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -2.57
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: Likely_benign. The variant received -5 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.8).
BP6
Variant 3-128879713-C-T is Benign according to our data. Variant chr3-128879713-C-T is described in ClinVar as Likely_benign. ClinVar VariationId is 1162190.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-2.57 with no splicing effect.
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 | MANE Select | c.22C>T | p.Leu8Leu | synonymous | Exon 1 of 18 | NP_054768.2 | |||
| ACAD9 | c.-254C>T | 5_prime_UTR_premature_start_codon_gain | Exon 1 of 17 | NP_001397734.1 | Q9H9W4 | ||||
| ACAD9 | c.-254C>T | 5_prime_UTR | Exon 1 of 17 | NP_001397734.1 | Q9H9W4 |
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| ACAD9 | TSL:1 MANE Select | c.22C>T | p.Leu8Leu | synonymous | Exon 1 of 18 | ENSP00000312618.7 | Q9H845 | ||
| ACAD9 | c.22C>T | p.Leu8Leu | synonymous | Exon 1 of 19 | ENSP00000505309.1 | A0A7P0T8U3 | |||
| ACAD9 | c.22C>T | p.Leu8Leu | synonymous | Exon 1 of 18 | ENSP00000504886.1 | A0A7P0T7Z1 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
33
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 6.85e-7 AC: 1AN: 1460602Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 726630 show subpopulations
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
AF:
AC:
1
AN:
1460602
Hom.:
Cov.:
31
AF XY:
AC XY:
1
AN XY:
726630
show subpopulations
African (AFR)
AF:
AC:
0
AN:
33456
American (AMR)
AF:
AC:
0
AN:
44712
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
26120
East Asian (EAS)
AF:
AC:
0
AN:
39694
South Asian (SAS)
AF:
AC:
0
AN:
86210
European-Finnish (FIN)
AF:
AC:
0
AN:
52934
Middle Eastern (MID)
AF:
AC:
0
AN:
5246
European-Non Finnish (NFE)
AF:
AC:
1
AN:
1111896
Other (OTH)
AF:
AC:
0
AN:
60334
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.425
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome
GnomAD4 genome
Cov.:
33
ClinVar
ClinVar submissions
View on ClinVar Significance:Likely benign
Revision:criteria provided, single submitter
Pathogenic
VUS
Benign
Condition
-
-
1
not provided (1)
Computational 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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