rs11629576

chr15-78214974-G-A

Variant summary

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

The NM_015162.5(ACSBG1):c.132-6872C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.536 in 151,974 control chromosomes in the GnomAD database, including 22,531 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 0.54 (22531 hom., cov: 32)
• Consequence: ACSBG1 NM_015162.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.489

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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.603 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ACSBG1	NM_015162.5	c.132-6872C>T		intron_variant		ENST00000258873.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ACSBG1	ENST00000258873.9	c.132-6872C>T		intron_variant		1	NM_015162.5	P1

Frequencies

GnomAD3 genomes AF: 0.536 AC: 81414 AN: 151856 Hom.: 22498 Cov.: 32

Gnomad AFR AF: 0.609

Gnomad AMI AF: 0.651

Gnomad AMR AF: 0.457

Gnomad ASJ AF: 0.472

Gnomad EAS AF: 0.160

Gnomad SAS AF: 0.362

Gnomad FIN AF: 0.553

Gnomad MID AF: 0.436

Gnomad NFE AF: 0.550

Gnomad OTH AF: 0.519

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

GnomAD4 genome AF: 0.536 AC: 81503 AN: 151974 Hom.: 22531 Cov.: 32 AF XY: 0.530 AC XY: 39384 AN XY: 74240

Gnomad4 AFR AF: 0.609

Gnomad4 AMR AF: 0.457

Gnomad4 ASJ AF: 0.472

Gnomad4 EAS AF: 0.161

Gnomad4 SAS AF: 0.363

Gnomad4 FIN AF: 0.553

Gnomad4 NFE AF: 0.550

Gnomad4 OTH AF: 0.518

Alfa AF: 0.545 Hom.: 38027

Bravo AF: 0.537

Asia WGS AF: 0.304 AC: 1060 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	0.98
Dann	Benign	0.65

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs11629576; hg19: chr15-78507316;