rs11629576

Variant names:

• chr15-78214974-G-A
• rs11629576
• NM_015162.5:c.132-6872C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 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=-0.95).
• 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 rank	MANE	Protein	UniProt
ACSBG1	NM_015162.5	c.132-6872C>T		intron_variant	Intron 1 of 13	ENST00000258873.9	NP_055977.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ACSBG1	ENST00000258873.9	c.132-6872C>T		intron_variant	Intron 1 of 13	1	NM_015162.5	ENSP00000258873.4

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

African (AFR) AF: 0.609 AC: 25248 AN: 41430

American (AMR) AF: 0.457 AC: 6979 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.472 AC: 1636 AN: 3466

East Asian (EAS) AF: 0.161 AC: 830 AN: 5162

South Asian (SAS) AF: 0.363 AC: 1745 AN: 4806

European-Finnish (FIN) AF: 0.553 AC: 5842 AN: 10562

Middle Eastern (MID) AF: 0.449 AC: 131 AN: 292

European-Non Finnish (NFE) AF: 0.550 AC: 37407 AN: 67952

Other (OTH) AF: 0.518 AC: 1094 AN: 2110

Alfa AF: 0.542 Hom.: 92909

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
PhyloP100		-0.49
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs11629576; hg19: chr15-78507316;