rs9304930

Positions:

• chr19-6158481-T-C

Variant summary

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

The ENST00000588485.6(ACSBG2):​c.507+1930T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.114 in 150,488 control chromosomes in the GnomAD database, including 1,985 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 0.11 (1985 hom., cov: 28)
• Consequence: ACSBG2 ENST00000588485.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.141

Genes affected

ACSBG2 (HGNC:24174): (acyl-CoA synthetase bubblegum family member 2) Enables acyl-CoA hydrolase activity and arachidonate-CoA ligase activity. Acts upstream of or within fatty acid metabolic process. Located in cytosol and mitochondrion. [provided by Alliance of Genome Resources, Apr 2022]

LOC105372255 (HGNC:):

RFX2 (HGNC:9983): (regulatory factor X2) This gene is a member of the regulatory factor X gene family, which encodes transcription factors that contain a highly-conserved winged helix DNA binding domain. The protein encoded by this gene is structurally related to regulatory factors X1, X3, X4, and X5. It is a transcriptional activator that can bind DNA as a monomer or as a heterodimer with other RFX family members. This protein can bind to cis elements in the promoter of the IL-5 receptor alpha gene. Two transcript variants encoding different isoforms have been described for this gene, and both variants utilize alternative polyadenylation sites. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.295 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ACSBG2	NM_030924.5	c.507+1930T>C		intron_variant		ENST00000588485.6	NP_112186.3
LOC105372255	XR_936282.3	n.218-10152A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ACSBG2	ENST00000588485.6	c.507+1930T>C		intron_variant		1	NM_030924.5	ENSP00000466336	P1

Frequencies

GnomAD3 genomes AF: 0.114 AC: 17171 AN: 150388 Hom.: 1977 Cov.: 28

Gnomad AFR AF: 0.300

Gnomad AMI AF: 0.0197

Gnomad AMR AF: 0.0553

Gnomad ASJ AF: 0.0490

Gnomad EAS AF: 0.0499

Gnomad SAS AF: 0.0721

Gnomad FIN AF: 0.0346

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0436

Gnomad OTH AF: 0.0849

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

GnomAD4 genome AF: 0.114 AC: 17214 AN: 150488 Hom.: 1985 Cov.: 28 AF XY: 0.112 AC XY: 8236 AN XY: 73570

Gnomad4 AFR AF: 0.300

Gnomad4 AMR AF: 0.0552

Gnomad4 ASJ AF: 0.0490

Gnomad4 EAS AF: 0.0496

Gnomad4 SAS AF: 0.0720

Gnomad4 FIN AF: 0.0346

Gnomad4 NFE AF: 0.0436

Gnomad4 OTH AF: 0.0897

Alfa AF: 0.0533 Hom.: 805

Bravo AF: 0.127

Asia WGS AF: 0.0910 AC: 317 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	5.4
DANN	Benign	0.26

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.060		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: rs9304930; hg19: chr19-6158492;