rs1533665

Positions:

• chr15-78238598-G-A
• chr15-78238598-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000560817.5(ACSBG1):​c.-64+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 ENST00000560817.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.14

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ACSBG1	ENST00000560817.5	c.-64+6671C>T		intron_variant		5
ACSBG1	ENST00000558793.1	n.420+6671C>T		intron_variant, non_coding_transcript_variant		4
ACSBG1	ENST00000558828.5	n.420+6671C>T		intron_variant, non_coding_transcript_variant		4

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

Gnomad4 AFR AF: 0.671

Gnomad4 AMR AF: 0.567

Gnomad4 ASJ AF: 0.680

Gnomad4 EAS AF: 0.726

Gnomad4 SAS AF: 0.695

Gnomad4 FIN AF: 0.574

Gnomad4 NFE AF: 0.628

Gnomad4 OTH AF: 0.634

Alfa AF: 0.633 Hom.: 35040

Bravo AF: 0.638

Asia WGS AF: 0.698 AC: 2429 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	6.7
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1533665; hg19: chr15-78530940;