chr15-78169115-A-G
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_015162.5(ACSBG1):c.*2329T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0683 in 606,398 control chromosomes in the GnomAD database, including 1,945 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.058 ( 383 hom., cov: 32)
Exomes 𝑓: 0.072 ( 1562 hom. )
Consequence
ACSBG1
NM_015162.5 3_prime_UTR
NM_015162.5 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.596
Genes affected
IDH3A (HGNC:5384): (isocitrate dehydrogenase (NAD(+)) 3 catalytic subunit alpha) Isocitrate dehydrogenases catalyze the oxidative decarboxylation of isocitrate to 2-oxoglutarate. These enzymes belong to two distinct subclasses, one of which utilizes NAD(+) as the electron acceptor and the other NADP(+). Five isocitrate dehydrogenases have been reported: three NAD(+)-dependent isocitrate dehydrogenases, which localize to the mitochondrial matrix, and two NADP(+)-dependent isocitrate dehydrogenases, one of which is mitochondrial and the other predominantly cytosolic. NAD(+)-dependent isocitrate dehydrogenases catalyze the allosterically regulated rate-limiting step of the tricarboxylic acid cycle. Each isozyme is a heterotetramer that is composed of two alpha subunits, one beta subunit, and one gamma subunit. The protein encoded by this gene is the alpha subunit of one isozyme of NAD(+)-dependent isocitrate dehydrogenase. [provided by RefSeq, Jul 2008]
ACSBG1 (HGNC:29567): (acyl-CoA synthetase bubblegum family member 1) The protein encoded by this gene possesses long-chain acyl-CoA synthetase activity. It is thought to play a central role in brain very long-chain fatty acids metabolism and myelinogenesis. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.67).
BP6
?
Variant 15-78169115-A-G is Benign according to our data. Variant chr15-78169115-A-G is described in ClinVar as [Benign]. Clinvar id is 1230438.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0841 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IDH3A | NM_005530.3 | c.*110A>G | 3_prime_UTR_variant | 11/11 | ENST00000299518.7 | ||
ACSBG1 | NM_015162.5 | c.*2329T>C | 3_prime_UTR_variant | 14/14 | ENST00000258873.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ACSBG1 | ENST00000258873.9 | c.*2329T>C | 3_prime_UTR_variant | 14/14 | 1 | NM_015162.5 | P1 | ||
IDH3A | ENST00000299518.7 | c.*110A>G | 3_prime_UTR_variant | 11/11 | 1 | NM_005530.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0576 AC: 8759AN: 152154Hom.: 383 Cov.: 32
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GnomAD4 exome AF: 0.0719 AC: 32653AN: 454126Hom.: 1562 Cov.: 7 AF XY: 0.0710 AC XY: 16994AN XY: 239420
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GnomAD4 genome ? AF: 0.0575 AC: 8757AN: 152272Hom.: 383 Cov.: 32 AF XY: 0.0585 AC XY: 4352AN XY: 74440
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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 | GeneDx | May 12, 2021 | - - |
Computational scores
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at