chr15-78178812-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_015162.5(ACSBG1):c.1504G>A(p.Gly502Ser) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000329 in 1,612,632 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 0.00014 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000021 ( 0 hom. )
Consequence
ACSBG1
NM_015162.5 missense
NM_015162.5 missense
Scores
3
12
4
Clinical Significance
Conservation
PhyloP100: 7.81
Genes affected
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 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, 0.872
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ACSBG1 | NM_015162.5 | c.1504G>A | p.Gly502Ser | missense_variant | 11/14 | ENST00000258873.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ACSBG1 | ENST00000258873.9 | c.1504G>A | p.Gly502Ser | missense_variant | 11/14 | 1 | NM_015162.5 | P1 | |
ACSBG1 | ENST00000560817.5 | c.778G>A | p.Gly260Ser | missense_variant | 7/10 | 5 | |||
ACSBG1 | ENST00000558301.5 | n.580G>A | non_coding_transcript_exon_variant | 3/3 | 5 | ||||
ACSBG1 | ENST00000560124.5 | c.*816G>A | 3_prime_UTR_variant, NMD_transcript_variant | 7/10 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.000145 AC: 22AN: 152206Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000362 AC: 9AN: 248936Hom.: 0 AF XY: 0.0000371 AC XY: 5AN XY: 134852
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GnomAD4 exome AF: 0.0000212 AC: 31AN: 1460308Hom.: 0 Cov.: 31 AF XY: 0.0000206 AC XY: 15AN XY: 726490
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GnomAD4 genome ? AF: 0.000144 AC: 22AN: 152324Hom.: 0 Cov.: 32 AF XY: 0.000148 AC XY: 11AN XY: 74480
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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 | Jan 23, 2023 | The c.1504G>A (p.G502S) alteration is located in exon 11 (coding exon 11) of the ACSBG1 gene. This alteration results from a G to A substitution at nucleotide position 1504, causing the glycine (G) at amino acid position 502 to be replaced by a serine (S). 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
Uncertain
D
BayesDel_noAF
Uncertain
Cadd
Pathogenic
Dann
Uncertain
DEOGEN2
Uncertain
T;T
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
D;D
M_CAP
Benign
D
MetaRNN
Pathogenic
D;D
MetaSVM
Benign
T
MutationAssessor
Uncertain
M;.
MutationTaster
Benign
D;D;D
PrimateAI
Uncertain
T
PROVEAN
Pathogenic
D;D
REVEL
Uncertain
Sift
Uncertain
D;D
Sift4G
Uncertain
D;T
Polyphen
D;.
Vest4
MutPred
Loss of methylation at K506 (P = 0.1497);.;
MVP
MPC
ClinPred
D
GERP RS
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