chr2-110949828-C-T

Variant names:

• chr2-110949828-C-T
• rs3789119
• NM_001142807.4:c.1059+16186C>T

Variant summary

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

The NM_001142807.4(ACOXL):​c.1059+16186C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.275 in 151,812 control chromosomes in the GnomAD database, including 5,896 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 0.28 (5896 hom., cov: 31)
• Consequence: ACOXL NM_001142807.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.234
• Publications: 6 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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.32 is higher than 0.05.

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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ACOXL	NM_001142807.4	MANE Select	c.1059+16186C>T		intron	N/A	NP_001136279.1
	ACOXL	NM_001437600.1		c.1060-13796C>T		intron	N/A	NP_001424529.1
	ACOXL	NM_001371254.1		c.1060-13796C>T		intron	N/A	NP_001358183.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ACOXL	ENST00000439055.6	TSL:2 MANE Select	c.1059+16186C>T		intron	N/A	ENSP00000407761.1
	ACOXL	ENST00000417074.5	TSL:1	c.573+16186C>T		intron	N/A	ENSP00000387832.1
	ACOXL	ENST00000676595.2		c.1060-13796C>T		intron	N/A	ENSP00000503683.1

Frequencies

GnomAD3 genomes AF: 0.275 AC: 41707 AN: 151694 Hom.: 5885 Cov.: 31

Gnomad AFR AF: 0.325

Gnomad AMI AF: 0.158

Gnomad AMR AF: 0.276

Gnomad ASJ AF: 0.270

Gnomad EAS AF: 0.317

Gnomad SAS AF: 0.271

Gnomad FIN AF: 0.256

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.247

Gnomad OTH AF: 0.256

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

GnomAD4 genome AF: 0.275 AC: 41749 AN: 151812 Hom.: 5896 Cov.: 31 AF XY: 0.275 AC XY: 20408 AN XY: 74196

African (AFR) AF: 0.325 AC: 13442 AN: 41390

American (AMR) AF: 0.276 AC: 4205 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.270 AC: 937 AN: 3468

East Asian (EAS) AF: 0.318 AC: 1638 AN: 5158

South Asian (SAS) AF: 0.270 AC: 1300 AN: 4816

European-Finnish (FIN) AF: 0.256 AC: 2688 AN: 10498

Middle Eastern (MID) AF: 0.282 AC: 83 AN: 294

European-Non Finnish (NFE) AF: 0.247 AC: 16764 AN: 67910

Other (OTH) AF: 0.259 AC: 548 AN: 2112

Alfa AF: 0.254 Hom.: 19167

Bravo AF: 0.275

Asia WGS AF: 0.303 AC: 1054 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.3
DANN	Benign	0.68
PhyloP100		-0.23
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: rs3789119; hg19: chr2-111707405;