GeneBe

12-120739440-C-A

Variant names:

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_000017.4(ACADS):​c.1231C>A​(p.Arg411Arg) variant causes a synonymous change. The variant allele was found at a frequency of 0.000000686 in 1,457,182 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 33)
Exomes 𝑓: 6.9e-7 ( 0 hom. )

Consequence

ACADS
NM_000017.4 synonymous

Scores

1
1

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 5.87

Publications

0 publications found
Variant links:
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 deficiency
    Inheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae), G2P, PanelApp Australia, Orphanet, ClinGen

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
ACADSNM_000017.4 linkc.1231C>A p.Arg411Arg synonymous_variant Exon 10 of 10 ENST00000242592.9 NP_000008.1 P16219E5KSD5
ACADSNM_001302554.2 linkc.1219C>A p.Arg407Arg synonymous_variant Exon 10 of 10 NP_001289483.1 P16219E9PE82B4DUH1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ACADSENST00000242592.9 linkc.1231C>A p.Arg411Arg synonymous_variant Exon 10 of 10 1 NM_000017.4 ENSP00000242592.4 P16219
ACADSENST00000411593.2 linkc.1219C>A p.Arg407Arg synonymous_variant Exon 10 of 10 2 ENSP00000401045.2 E9PE82
ENSG00000255946ENST00000724268.1 linkn.305-9152G>T intron_variant Intron 1 of 1

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
AF:
6.86e-7
AC:
1
AN:
1457182
Hom.:
0
Cov.:
33
AF XY:
0.00
AC XY:
0
AN XY:
724876
show subpopulations
African (AFR)
AF:
0.00
AC:
0
AN:
33438
American (AMR)
AF:
0.00
AC:
0
AN:
44656
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
26082
East Asian (EAS)
AF:
0.00
AC:
0
AN:
39670
South Asian (SAS)
AF:
0.00
AC:
0
AN:
86184
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
50038
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
5500
European-Non Finnish (NFE)
AF:
9.00e-7
AC:
1
AN:
1111394
Other (OTH)
AF:
0.00
AC:
0
AN:
60220
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.475
Heterozygous variant carriers
0
0
1
1
2
2
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
Cov.:
33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Uncertain
-0.030
CADD
Benign
12
DANN
Benign
0.92
PhyloP100
5.9

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs369416846; hg19: chr12-121177243; API