rs79530903
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_014049.5(ACAD9):āc.988A>Cā(p.Lys330Gln) variant causes a missense change. The variant allele was found at a frequency of 0.00107 in 1,614,238 control chromosomes in the GnomAD database, including 26 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ). Synonymous variant affecting the same amino acid position (i.e. K330K) has been classified as Likely benign.
Frequency
Consequence
NM_014049.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ACAD9 | NM_014049.5 | c.988A>C | p.Lys330Gln | missense_variant | 10/18 | ENST00000308982.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ACAD9 | ENST00000308982.12 | c.988A>C | p.Lys330Gln | missense_variant | 10/18 | 1 | NM_014049.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00143 AC: 217AN: 152226Hom.: 9 Cov.: 33
GnomAD3 exomes AF: 0.00221 AC: 555AN: 251462Hom.: 11 AF XY: 0.00212 AC XY: 288AN XY: 135920
GnomAD4 exome AF: 0.00104 AC: 1517AN: 1461894Hom.: 17 Cov.: 31 AF XY: 0.00106 AC XY: 768AN XY: 727248
GnomAD4 genome AF: 0.00143 AC: 218AN: 152344Hom.: 9 Cov.: 33 AF XY: 0.00138 AC XY: 103AN XY: 74496
ClinVar
Submissions by phenotype
Acyl-CoA dehydrogenase 9 deficiency Benign:4
Benign, no assertion criteria provided | clinical testing | Natera, Inc. | Dec 16, 2019 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Aug 17, 2021 | - - |
Benign, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Oct 26, 2023 | - - |
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Apr 27, 2017 | This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases was too high to be consistent with this variant causing disease. Therefore, this variant is classified as benign. - |
not provided Benign:3
Likely benign, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | Jun 02, 2015 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Nov 01, 2023 | ACAD9: BS1, BS2 - |
not specified Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | Apr 30, 2013 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
Likely benign, criteria provided, single submitter | clinical testing | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | May 03, 2022 | - - |
ACAD9-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jun 29, 2020 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at