15-78233652-G-A

Variant names:

• chr15-78233652-G-A
• rs11634386
• NM_015162.5:c.131+719C>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.131+719C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.199 in 152,104 control chromosomes in the GnomAD database, including 3,143 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 0.20 (3143 hom., cov: 33)
• Consequence: ACSBG1 NM_015162.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0770
• Publications: 3 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=-0.85).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.239 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ACSBG1	NM_015162.5	c.131+719C>T		intron_variant	Intron 1 of 13	ENST00000258873.9	NP_055977.3
ACSBG1	NM_001199377.2	c.131+719C>T		intron_variant	Intron 1 of 13		NP_001186306.1
ACSBG1	XM_017022025.3	c.131+719C>T		intron_variant	Intron 1 of 14		XP_016877514.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ACSBG1	ENST00000258873.9	c.131+719C>T		intron_variant	Intron 1 of 13	1	NM_015162.5	ENSP00000258873.4

Frequencies

GnomAD3 genomes AF: 0.199 AC: 30293 AN: 151986 Hom.: 3142 Cov.: 33

Gnomad AFR AF: 0.238

Gnomad AMI AF: 0.276

Gnomad AMR AF: 0.246

Gnomad ASJ AF: 0.224

Gnomad EAS AF: 0.216

Gnomad SAS AF: 0.214

Gnomad FIN AF: 0.105

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.175

Gnomad OTH AF: 0.218

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

GnomAD4 genome AF: 0.199 AC: 30305 AN: 152104 Hom.: 3143 Cov.: 33 AF XY: 0.198 AC XY: 14763 AN XY: 74378

African (AFR) AF: 0.238 AC: 9874 AN: 41492

American (AMR) AF: 0.245 AC: 3742 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.224 AC: 779 AN: 3472

East Asian (EAS) AF: 0.216 AC: 1116 AN: 5166

South Asian (SAS) AF: 0.213 AC: 1026 AN: 4818

European-Finnish (FIN) AF: 0.105 AC: 1113 AN: 10592

Middle Eastern (MID) AF: 0.259 AC: 76 AN: 294

European-Non Finnish (NFE) AF: 0.175 AC: 11872 AN: 67990

Other (OTH) AF: 0.216 AC: 456 AN: 2110

Alfa AF: 0.191 Hom.: 4773

Bravo AF: 0.214

Asia WGS AF: 0.209 AC: 725 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.7
DANN	Benign	0.88
PhyloP100		0.077
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: rs11634386; hg19: chr15-78525994;