rs1002016

Variant names:

• chr2-110859335-G-A
• rs1002016
• NM_001142807.4:c.788+17930G>A

Variant summary

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

The NM_001142807.4(ACOXL):​c.788+17930G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.181 in 152,098 control chromosomes in the GnomAD database, including 2,661 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 0.18 (2661 hom., cov: 32)
• Consequence: ACOXL NM_001142807.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.116
• Publications: 4 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.232 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.788+17930G>A		intron	N/A	NP_001136279.1
	ACOXL	NM_001437600.1		c.788+17930G>A		intron	N/A	NP_001424529.1
	ACOXL	NM_001371254.1		c.788+17930G>A		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.788+17930G>A		intron	N/A	ENSP00000407761.1
	ACOXL	ENST00000417074.5	TSL:1	c.302+17930G>A		intron	N/A	ENSP00000387832.1
	ACOXL	ENST00000340561.8	TSL:1	c.788+17930G>A		intron	N/A	ENSP00000343717.4

Frequencies

GnomAD3 genomes AF: 0.180 AC: 27425 AN: 151978 Hom.: 2650 Cov.: 32

Gnomad AFR AF: 0.235

Gnomad AMI AF: 0.0417

Gnomad AMR AF: 0.212

Gnomad ASJ AF: 0.157

Gnomad EAS AF: 0.208

Gnomad SAS AF: 0.201

Gnomad FIN AF: 0.132

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.148

Gnomad OTH AF: 0.163

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

GnomAD4 genome AF: 0.181 AC: 27473 AN: 152098 Hom.: 2661 Cov.: 32 AF XY: 0.182 AC XY: 13543 AN XY: 74358

African (AFR) AF: 0.236 AC: 9776 AN: 41462

American (AMR) AF: 0.212 AC: 3242 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.157 AC: 546 AN: 3472

East Asian (EAS) AF: 0.208 AC: 1075 AN: 5166

South Asian (SAS) AF: 0.199 AC: 957 AN: 4820

European-Finnish (FIN) AF: 0.132 AC: 1392 AN: 10576

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.148 AC: 10055 AN: 67988

Other (OTH) AF: 0.168 AC: 356 AN: 2114

Alfa AF: 0.160 Hom.: 4019

Bravo AF: 0.184

Asia WGS AF: 0.244 AC: 850 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.98
DANN	Benign	0.71
PhyloP100		-0.12
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: rs1002016; hg19: chr2-111616912;