rs9304930

Variant names:

• chr19-6158481-T-C
• rs9304930
• NM_030924.5:c.507+1930T>C

Variant summary

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

The NM_030924.5(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 NM_030924.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.141
• Publications: 1 publications found

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]

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]

RFX2 Gene-Disease associations (from GenCC):

• cerebral palsy

  Inheritance: AD Classification: LIMITED Submitted by: Ambry Genetics

LOC105372255 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_030924.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ACSBG2	NM_030924.5	MANE Select	c.507+1930T>C		intron	N/A	NP_112186.3
	ACSBG2	NM_001289177.2		c.507+1930T>C		intron	N/A	NP_001276106.1
	ACSBG2	NM_001289178.2		c.507+1930T>C		intron	N/A	NP_001276107.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ACSBG2	ENST00000588485.6	TSL:1 MANE Select	c.507+1930T>C		intron	N/A	ENSP00000466336.2
	ACSBG2	ENST00000591403.5	TSL:1	c.507+1930T>C		intron	N/A	ENSP00000467755.1
	ACSBG2	ENST00000588304.5	TSL:1	c.357+1930T>C		intron	N/A	ENSP00000464938.1

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

African (AFR) AF: 0.300 AC: 12056 AN: 40192

American (AMR) AF: 0.0552 AC: 838 AN: 15188

Ashkenazi Jewish (ASJ) AF: 0.0490 AC: 170 AN: 3472

East Asian (EAS) AF: 0.0496 AC: 257 AN: 5178

South Asian (SAS) AF: 0.0720 AC: 344 AN: 4780

European-Finnish (FIN) AF: 0.0346 AC: 362 AN: 10460

Middle Eastern (MID) AF: 0.0719 AC: 21 AN: 292

European-Non Finnish (NFE) AF: 0.0436 AC: 2960 AN: 67918

Other (OTH) AF: 0.0897 AC: 188 AN: 2096

Alfa AF: 0.0639 Hom.: 2811

Bravo AF: 0.127

Asia WGS AF: 0.0910 AC: 317 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	5.4
DANN	Benign	0.26
PhyloP100		-0.14
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs9304930; hg19: chr19-6158492;