rs1800556
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The ENST00000242592.9(ACADS):c.511C>T(p.Arg171Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0413 in 1,613,908 control chromosomes in the GnomAD database, including 1,595 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
ENST00000242592.9 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ACADS | NM_000017.4 | c.511C>T | p.Arg171Trp | missense_variant | 5/10 | ENST00000242592.9 | NP_000008.1 | |
ACADS | NM_001302554.2 | c.473-174C>T | intron_variant | NP_001289483.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ACADS | ENST00000242592.9 | c.511C>T | p.Arg171Trp | missense_variant | 5/10 | 1 | NM_000017.4 | ENSP00000242592 | P1 | |
ACADS | ENST00000411593.2 | c.473-174C>T | intron_variant | 2 | ENSP00000401045 |
Frequencies
GnomAD3 genomes AF: 0.0316 AC: 4806AN: 152058Hom.: 103 Cov.: 33
GnomAD3 exomes AF: 0.0309 AC: 7750AN: 250994Hom.: 183 AF XY: 0.0310 AC XY: 4212AN XY: 135720
GnomAD4 exome AF: 0.0423 AC: 61903AN: 1461732Hom.: 1492 Cov.: 33 AF XY: 0.0414 AC XY: 30070AN XY: 727170
GnomAD4 genome AF: 0.0316 AC: 4805AN: 152176Hom.: 103 Cov.: 33 AF XY: 0.0315 AC XY: 2345AN XY: 74386
ClinVar
Submissions by phenotype
Deficiency of butyryl-CoA dehydrogenase Pathogenic:1Benign:6Other:2
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Nov 07, 2021 | - - |
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Mar 06, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. - |
Pathogenic, no assertion criteria provided | literature only | OMIM | Jan 01, 2001 | - - |
not provided, no classification provided | phenotyping only | GenomeConnect, ClinGen | - | The variant was identified in multiple GenomeConnect participants. Variant interpreted as Uncertain significance and reported on 05-17-2017 by Lab or GTR ID 303161. Variant was interpreted as Pathogenic and reported on 10-02-2015 by Lab or GTR ID 26957. GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant. - |
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Dec 30, 2019 | - - |
Benign, criteria provided, single submitter | clinical testing | Mendelics | Aug 22, 2023 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Victorian Clinical Genetics Services, Murdoch Childrens Research Institute | Feb 02, 2022 | Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as likely benign. Following criteria are met: 0308 - Population frequency for this variant is out of keeping with known incidence of acyl-CoA dehydrogenase, short-chain, deficiency of (MIM#201470). (SB) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign - |
Benign, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Nov 27, 2023 | - - |
not provided, no classification provided | literature only | GeneReviews | - | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jan 04, 2018 | This variant is associated with the following publications: (PMID: 29555771, 29678161, 28532786, 18523805, 9499414, 11134486, 16926354, 12220177) - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at