chr3-132561166-G-A
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Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_032169.5(ACAD11):c.2053C>T(p.Arg685Cys) variant causes a missense change. The variant allele was found at a frequency of 0.0000161 in 1,613,518 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.000020 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000016 ( 0 hom. )
Consequence
ACAD11
NM_032169.5 missense
NM_032169.5 missense
Scores
14
2
2
Clinical Significance
Conservation
PhyloP100: 3.88
Genes affected
ACAD11 (HGNC:30211): (acyl-CoA dehydrogenase family member 11) This gene encodes an acyl-CoA dehydrogenase enzyme with a preference for carbon chain lengths between 20 and 26. Naturally occurring read-through transcription occurs between the upstream gene NPHP3 (nephronophthisis 3 (adolescent)) and this gene. [provided by RefSeq, Aug 2015]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 4 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
PP3
MetaRNN computational evidence supports a deleterious effect, 0.917
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ACAD11 | NM_032169.5 | c.2053C>T | p.Arg685Cys | missense_variant | 18/20 | ENST00000264990.11 | |
NPHP3-ACAD11 | NR_037804.1 | n.6665C>T | non_coding_transcript_exon_variant | 43/45 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ACAD11 | ENST00000264990.11 | c.2053C>T | p.Arg685Cys | missense_variant | 18/20 | 1 | NM_032169.5 | P1 | |
ACAD11 | ENST00000485198.5 | c.*534C>T | 3_prime_UTR_variant, NMD_transcript_variant | 16/18 | 1 | ||||
ACAD11 | ENST00000469042.5 | n.2839C>T | non_coding_transcript_exon_variant | 16/18 | 2 | ||||
ACAD11 | ENST00000496418.5 | n.2561C>T | non_coding_transcript_exon_variant | 17/19 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152012Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000199 AC: 5AN: 250986Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135626
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GnomAD4 exome AF: 0.0000157 AC: 23AN: 1461388Hom.: 0 Cov.: 30 AF XY: 0.0000206 AC XY: 15AN XY: 726994
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GnomAD4 genome AF: 0.0000197 AC: 3AN: 152130Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74366
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 18, 2022 | The c.2053C>T (p.R685C) alteration is located in exon 18 (coding exon 18) of the ACAD11 gene. This alteration results from a C to T substitution at nucleotide position 2053, causing the arginine (R) at amino acid position 685 to be replaced by a cysteine (C). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Pathogenic
CADD
Pathogenic
DANN
Pathogenic
DEOGEN2
Pathogenic
D
Eigen
Pathogenic
Eigen_PC
Pathogenic
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D
M_CAP
Pathogenic
D
MetaRNN
Pathogenic
D
MetaSVM
Pathogenic
D
MutationAssessor
Pathogenic
H
MutationTaster
Benign
D;D;D
PROVEAN
Pathogenic
D
REVEL
Pathogenic
Sift
Pathogenic
D
Sift4G
Pathogenic
D
Polyphen
D
Vest4
MutPred
Loss of MoRF binding (P = 0.003);
MVP
MPC
ClinPred
D
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at