chr15-78173606-C-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBS1BS2
The NM_015162.5(ACSBG1):c.2076G>A(p.Ser692=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00259 in 1,614,102 control chromosomes in the GnomAD database, including 76 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.014 ( 42 hom., cov: 32)
Exomes 𝑓: 0.0014 ( 34 hom. )
Consequence
ACSBG1
NM_015162.5 synonymous
NM_015162.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -2.97
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 -10 ACMG points.
BP6
?
Variant 15-78173606-C-T is Benign according to our data. Variant chr15-78173606-C-T is described in ClinVar as [Benign]. Clinvar id is 718037.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0137 (2080/152276) while in subpopulation AFR AF= 0.0475 (1972/41532). AF 95% confidence interval is 0.0457. There are 42 homozygotes in gnomad4. There are 988 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 42 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ACSBG1 | NM_015162.5 | c.2076G>A | p.Ser692= | synonymous_variant | 13/14 | ENST00000258873.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ACSBG1 | ENST00000258873.9 | c.2076G>A | p.Ser692= | synonymous_variant | 13/14 | 1 | NM_015162.5 | P1 | |
ACSBG1 | ENST00000560817.5 | c.1350G>A | p.Ser450= | synonymous_variant | 9/10 | 5 | |||
ACSBG1 | ENST00000560183.1 | n.662G>A | non_coding_transcript_exon_variant | 2/2 | 2 | ||||
ACSBG1 | ENST00000560124.5 | c.*1388G>A | 3_prime_UTR_variant, NMD_transcript_variant | 9/10 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0137 AC: 2077AN: 152158Hom.: 42 Cov.: 32
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GnomAD3 exomes AF: 0.00363 AC: 911AN: 251246Hom.: 17 AF XY: 0.00271 AC XY: 368AN XY: 135826
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GnomAD4 exome AF: 0.00144 AC: 2105AN: 1461826Hom.: 34 Cov.: 30 AF XY: 0.00121 AC XY: 877AN XY: 727208
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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 21, 2018 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
DS_DG_spliceai
Position offset: -1
Find out detailed SpliceAI scores and Pangolin per-transcript scores at