NM_015162.5:c.132-10375C>A

Variant names:

• chr15-78218477-G-T
• rs11072744
• NM_015162.5:c.132-10375C>A

Variant summary

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

The NM_015162.5(ACSBG1):​c.132-10375C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.216 in 152,110 control chromosomes in the GnomAD database, including 3,580 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 0.22 (3580 hom., cov: 31)
• Consequence: ACSBG1 NM_015162.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0460
• Publications: 2 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.22 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ACSBG1	NM_015162.5	c.132-10375C>A		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.132-10375C>A		intron_variant	Intron 1 of 13	1	NM_015162.5	ENSP00000258873.4

Frequencies

GnomAD3 genomes AF: 0.216 AC: 32789 AN: 151990 Hom.: 3577 Cov.: 31

Gnomad AFR AF: 0.224

Gnomad AMI AF: 0.178

Gnomad AMR AF: 0.207

Gnomad ASJ AF: 0.213

Gnomad EAS AF: 0.130

Gnomad SAS AF: 0.147

Gnomad FIN AF: 0.241

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.221

Gnomad OTH AF: 0.213

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

GnomAD4 genome AF: 0.216 AC: 32810 AN: 152110 Hom.: 3580 Cov.: 31 AF XY: 0.215 AC XY: 15970 AN XY: 74352

African (AFR) AF: 0.224 AC: 9284 AN: 41486

American (AMR) AF: 0.207 AC: 3166 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.213 AC: 740 AN: 3470

East Asian (EAS) AF: 0.130 AC: 675 AN: 5182

South Asian (SAS) AF: 0.147 AC: 707 AN: 4824

European-Finnish (FIN) AF: 0.241 AC: 2545 AN: 10562

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.221 AC: 15041 AN: 67980

Other (OTH) AF: 0.212 AC: 447 AN: 2112

Alfa AF: 0.223 Hom.: 11187

Bravo AF: 0.216

Asia WGS AF: 0.168 AC: 588 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.5
DANN	Benign	0.76
PhyloP100		0.046
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: rs11072744; hg19: chr15-78510819; COSMIC: COSV51910073; COSMIC: COSV51910073;