chr15-78173669-G-A
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2
The NM_015162.5(ACSBG1):c.2013C>T(p.Asn671=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00142 in 1,614,194 control chromosomes in the GnomAD database, including 33 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0073 ( 15 hom., cov: 32)
Exomes 𝑓: 0.00081 ( 18 hom. )
Consequence
ACSBG1
NM_015162.5 synonymous
NM_015162.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -4.54
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 Benign. Variant got -15 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BP6
?
Variant 15-78173669-G-A is Benign according to our data. Variant chr15-78173669-G-A is described in ClinVar as [Benign]. Clinvar id is 785502.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-4.54 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00726 (1106/152308) while in subpopulation AFR AF= 0.0256 (1064/41568). AF 95% confidence interval is 0.0243. There are 15 homozygotes in gnomad4. There are 520 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 15 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ACSBG1 | NM_015162.5 | c.2013C>T | p.Asn671= | synonymous_variant | 13/14 | ENST00000258873.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ACSBG1 | ENST00000258873.9 | c.2013C>T | p.Asn671= | synonymous_variant | 13/14 | 1 | NM_015162.5 | P1 | |
ACSBG1 | ENST00000560817.5 | c.1287C>T | p.Asn429= | synonymous_variant | 9/10 | 5 | |||
ACSBG1 | ENST00000560183.1 | n.599C>T | non_coding_transcript_exon_variant | 2/2 | 2 | ||||
ACSBG1 | ENST00000560124.5 | c.*1325C>T | 3_prime_UTR_variant, NMD_transcript_variant | 9/10 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00726 AC: 1105AN: 152190Hom.: 15 Cov.: 32
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GnomAD3 exomes AF: 0.00188 AC: 472AN: 251486Hom.: 7 AF XY: 0.00152 AC XY: 206AN XY: 135920
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GnomAD4 exome AF: 0.000810 AC: 1184AN: 1461886Hom.: 18 Cov.: 31 AF XY: 0.000704 AC XY: 512AN XY: 727246
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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 | May 09, 2018 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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