chr3-132605177-C-T
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Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_ModerateBP7BS2_Supporting
The NM_032169.5(ACAD11):c.1443G>A(p.Leu481=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0005 in 1,613,242 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.00044 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00051 ( 2 hom. )
Consequence
ACAD11
NM_032169.5 synonymous
NM_032169.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.0670
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]
ACKR4 (HGNC:1611): (atypical chemokine receptor 4) The protein encoded by this gene is a member of the G protein-coupled receptor family, and is a receptor for C-C type chemokines. This receptor has been shown to bind dendritic cell- and T cell-activated chemokines including CCL19/ELC, CCL21/SLC, and CCL25/TECK. A pseudogene of this gene is found on chromosome 6. Alternatively spliced transcript variants encoding the same protein have been described. [provided by RefSeq, Jul 2013]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.43).
BP7
Synonymous conserved (PhyloP=-0.067 with no splicing effect.
BS2
High Homozygotes in GnomAdExome4 at 2 AR geneVariant has number of homozygotes lower than other variant known as pathogenic in the gene, so the strength is limited to Supporting.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ACAD11 | NM_032169.5 | c.1443G>A | p.Leu481= | synonymous_variant | 12/20 | ENST00000264990.11 | |
NPHP3-ACAD11 | NR_037804.1 | n.5445G>A | non_coding_transcript_exon_variant | 38/45 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ACAD11 | ENST00000264990.11 | c.1443G>A | p.Leu481= | synonymous_variant | 12/20 | 1 | NM_032169.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000440 AC: 67AN: 152164Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000378 AC: 95AN: 251214Hom.: 0 AF XY: 0.000427 AC XY: 58AN XY: 135758
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GnomAD4 exome AF: 0.000506 AC: 740AN: 1461078Hom.: 2 Cov.: 30 AF XY: 0.000475 AC XY: 345AN XY: 726842
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GnomAD4 genome AF: 0.000440 AC: 67AN: 152164Hom.: 0 Cov.: 32 AF XY: 0.000363 AC XY: 27AN XY: 74334
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Nov 11, 2013 | - - |
Computational scores
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BayesDel_noAF
Benign
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Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at