15-78238598-G-A

Variant names:

• chr15-78238598-G-A
• rs1533665
• ENST00000560817.5:c.-64+6671C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000558793.1(ACSBG1):​n.420+6671C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.636 in 152,108 control chromosomes in the GnomAD database, including 31,010 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.64 (31010 hom., cov: 33)
• Consequence: ACSBG1 ENST00000558793.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.14
• Publications: 14 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.706 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000558793.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ACSBG1	ENST00000560817.5	TSL:5	c.-64+6671C>T		intron	N/A	ENSP00000453451.1	F5H4U6
	ACSBG1	ENST00000558793.1	TSL:4	n.420+6671C>T		intron	N/A
	ACSBG1	ENST00000558828.5	TSL:4	n.420+6671C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.636 AC: 96736 AN: 151990 Hom.: 30986 Cov.: 33

Gnomad AFR AF: 0.671

Gnomad AMI AF: 0.567

Gnomad AMR AF: 0.568

Gnomad ASJ AF: 0.680

Gnomad EAS AF: 0.726

Gnomad SAS AF: 0.695

Gnomad FIN AF: 0.574

Gnomad MID AF: 0.680

Gnomad NFE AF: 0.628

Gnomad OTH AF: 0.637

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.636 AC: 96801 AN: 152108 Hom.: 31010 Cov.: 33 AF XY: 0.632 AC XY: 46968 AN XY: 74332

African (AFR) AF: 0.671 AC: 27847 AN: 41478

American (AMR) AF: 0.567 AC: 8670 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.680 AC: 2358 AN: 3468

East Asian (EAS) AF: 0.726 AC: 3764 AN: 5186

South Asian (SAS) AF: 0.695 AC: 3349 AN: 4820

European-Finnish (FIN) AF: 0.574 AC: 6064 AN: 10560

Middle Eastern (MID) AF: 0.677 AC: 199 AN: 294

European-Non Finnish (NFE) AF: 0.628 AC: 42696 AN: 67998

Other (OTH) AF: 0.634 AC: 1338 AN: 2112

Alfa AF: 0.634 Hom.: 61058

Bravo AF: 0.638

Asia WGS AF: 0.698 AC: 2429 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	6.7
DANN	Benign	0.76
PhyloP100		1.1
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1533665;

hg19: chr15-78530940;