chr17-37088918-G-A
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_198834.3(ACACA):c.7028+20C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000189 in 1,614,024 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.00015 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00019 ( 5 hom. )
Consequence
ACACA
NM_198834.3 intron
NM_198834.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.0230
Genes affected
ACACA (HGNC:84): (acetyl-CoA carboxylase alpha) Acetyl-CoA carboxylase (ACC) is a complex multifunctional enzyme system. ACC is a biotin-containing enzyme which catalyzes the carboxylation of acetyl-CoA to malonyl-CoA, the rate-limiting step in fatty acid synthesis. There are two ACC forms, alpha and beta, encoded by two different genes. ACC-alpha is highly enriched in lipogenic tissues. The enzyme is under long term control at the transcriptional and translational levels and under short term regulation by the phosphorylation/dephosphorylation of targeted serine residues and by allosteric transformation by citrate or palmitoyl-CoA. Multiple alternatively spliced transcript variants divergent in the 5' sequence and encoding distinct isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BP6
?
Variant 17-37088918-G-A is Benign according to our data. Variant chr17-37088918-G-A is described in ClinVar as [Benign]. Clinvar id is 1987384.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
?
High AC in GnomAd at 24 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ACACA | NM_198834.3 | c.7028+20C>T | intron_variant | ENST00000616317.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ACACA | ENST00000616317.5 | c.7028+20C>T | intron_variant | 1 | NM_198834.3 |
Frequencies
GnomAD3 genomes ? AF: 0.000158 AC: 24AN: 152192Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000418 AC: 105AN: 251482Hom.: 1 AF XY: 0.000581 AC XY: 79AN XY: 135914
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GnomAD4 exome AF: 0.000193 AC: 282AN: 1461714Hom.: 5 Cov.: 32 AF XY: 0.000268 AC XY: 195AN XY: 727170
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GnomAD4 genome ? AF: 0.000151 AC: 23AN: 152310Hom.: 0 Cov.: 32 AF XY: 0.000242 AC XY: 18AN XY: 74494
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jul 06, 2023 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at