NM_000017.4:c.360+21C>G
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_000017.4(ACADS):c.360+21C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000894 in 1,565,598 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0000066 ( 0 hom., cov: 33)
Exomes 𝑓: 0.0000092 ( 0 hom. )
Consequence
ACADS
NM_000017.4 intron
NM_000017.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.0240
Publications
0 publications found
Genes affected
ACADS (HGNC:90): (acyl-CoA dehydrogenase short chain) This gene encodes a tetrameric mitochondrial flavoprotein, which is a member of the acyl-CoA dehydrogenase family. This enzyme catalyzes the initial step of the mitochondrial fatty acid beta-oxidation pathway. Mutations in this gene have been associated with short-chain acyl-CoA dehydrogenase (SCAD) deficiency. Alternative splicing results in two variants which encode different isoforms. [provided by RefSeq, Oct 2014]
ACADS Gene-Disease associations (from GenCC):
- short chain acyl-CoA dehydrogenase deficiencyInheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae), G2P, PanelApp Australia, Orphanet, ClinGen
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -4 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BP6
Variant 12-120737156-C-G is Benign according to our data. Variant chr12-120737156-C-G is described in ClinVar as Likely_benign. ClinVar VariationId is 254694.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ACADS | ENST00000242592.9 | c.360+21C>G | intron_variant | Intron 3 of 9 | 1 | NM_000017.4 | ENSP00000242592.4 | |||
ACADS | ENST00000539690.1 | n.493C>G | non_coding_transcript_exon_variant | Exon 3 of 3 | 2 | |||||
ACADS | ENST00000411593.2 | c.360+21C>G | intron_variant | Intron 3 of 9 | 2 | ENSP00000401045.2 | ||||
ENSG00000255946 | ENST00000724268.1 | n.305-6868G>C | intron_variant | Intron 1 of 1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152252Hom.: 0 Cov.: 33 show subpopulations
GnomAD3 genomes
AF:
AC:
1
AN:
152252
Hom.:
Cov.:
33
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
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Gnomad EAS
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Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
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Gnomad NFE
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Gnomad OTH
AF:
GnomAD2 exomes AF: 0.00000580 AC: 1AN: 172436 AF XY: 0.00 show subpopulations
GnomAD2 exomes
AF:
AC:
1
AN:
172436
AF XY:
Gnomad AFR exome
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Gnomad AMR exome
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Gnomad ASJ exome
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Gnomad EAS exome
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Gnomad FIN exome
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Gnomad NFE exome
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Gnomad OTH exome
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GnomAD4 exome AF: 0.00000920 AC: 13AN: 1413228Hom.: 0 Cov.: 34 AF XY: 0.0000129 AC XY: 9AN XY: 698694 show subpopulations
GnomAD4 exome
AF:
AC:
13
AN:
1413228
Hom.:
Cov.:
34
AF XY:
AC XY:
9
AN XY:
698694
show subpopulations
African (AFR)
AF:
AC:
0
AN:
32286
American (AMR)
AF:
AC:
0
AN:
37926
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
25368
East Asian (EAS)
AF:
AC:
0
AN:
36948
South Asian (SAS)
AF:
AC:
0
AN:
80782
European-Finnish (FIN)
AF:
AC:
0
AN:
49474
Middle Eastern (MID)
AF:
AC:
0
AN:
5702
European-Non Finnish (NFE)
AF:
AC:
13
AN:
1086280
Other (OTH)
AF:
AC:
0
AN:
58462
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.479
Heterozygous variant carriers
0
1
2
3
4
5
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
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Age
GnomAD4 genome AF: 0.00000656 AC: 1AN: 152370Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74520 show subpopulations
GnomAD4 genome
AF:
AC:
1
AN:
152370
Hom.:
Cov.:
33
AF XY:
AC XY:
1
AN XY:
74520
show subpopulations
African (AFR)
AF:
AC:
0
AN:
41596
American (AMR)
AF:
AC:
0
AN:
15308
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3472
East Asian (EAS)
AF:
AC:
0
AN:
5184
South Asian (SAS)
AF:
AC:
0
AN:
4834
European-Finnish (FIN)
AF:
AC:
0
AN:
10626
Middle Eastern (MID)
AF:
AC:
0
AN:
294
European-Non Finnish (NFE)
AF:
AC:
1
AN:
68032
Other (OTH)
AF:
AC:
0
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.625
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:
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Benign:1
-
PreventionGenetics, part of Exact Sciences
Significance:Likely benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
RBP_binding_hub_radar
RBP_regulation_power_radar
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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