2-111117769-CGG-GGT

Variant names:

• chr2-111117769-CGG-GGT
• NM_001142807.4:c.1696_1698delCGGinsGGT
• ACOXL p.Arg566Gly

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_001142807.4(ACOXL):​c.1696_1698delCGGinsGGT​(p.Arg566Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. It is difficult to determine the true allele frequency of this variant because it is of type MNV, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R566W) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 33)
• Consequence: ACOXL NM_001142807.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.38
• Publications: 0 publications found

Genes affected

ACOXL (HGNC:25621): (acyl-CoA oxidase like) Predicted to enable acyl-CoA oxidase activity; fatty acid binding activity; and flavin adenine dinucleotide binding activity. Predicted to be involved in fatty acid beta-oxidation using acyl-CoA oxidase and lipid homeostasis. Predicted to be located in peroxisomal matrix. Predicted to be active in peroxisome. [provided by Alliance of Genome Resources, Apr 2022]

MIR4435-2HG (HGNC:35163): (MIR4435-2 host gene)

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001142807.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ACOXL	NM_001142807.4	MANE Select	c.1696_1698delCGGinsGGT	p.Arg566Gly	missense	N/A	NP_001136279.1	Q9NUZ1-4
	ACOXL	NM_001437600.1		c.1786_1788delCGGinsGGT	p.Arg596Gly	missense	N/A	NP_001424529.1	A0A7I2V3X2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ACOXL	ENST00000439055.6	TSL:2 MANE Select	c.1696_1698delCGGinsGGT	p.Arg566Gly	missense	N/A	ENSP00000407761.1	Q9NUZ1-4
	ACOXL	ENST00000957119.1		c.1828_1830delCGGinsGGT	p.Arg610Gly	missense	N/A	ENSP00000627178.1
	ACOXL	ENST00000957116.1		c.1813_1815delCGGinsGGT	p.Arg605Gly	missense	N/A	ENSP00000627175.1

Frequencies

GnomAD3 genomes Cov.: 33

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

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		1.4

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

hg19: chr2-111875346;