2-111039954-C-T

Variant names:

• chr2-111039954-C-T
• rs3789080
• NM_001142807.4:c.1369+8240C>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.1369+8240C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.858 in 152,306 control chromosomes in the GnomAD database, including 56,534 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 0.86 (56534 hom., cov: 34)
• Consequence: ACOXL NM_001142807.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.278
• Publications: 12 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)

LOC124907866 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.943 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ACOXL	NM_001142807.4	c.1369+8240C>T		intron_variant	Intron 15 of 17	ENST00000439055.6	NP_001136279.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ACOXL	ENST00000439055.6	c.1369+8240C>T		intron_variant	Intron 15 of 17	2	NM_001142807.4	ENSP00000407761.1

Frequencies

GnomAD3 genomes AF: 0.859 AC: 130662 AN: 152188 Hom.: 56500 Cov.: 34

Gnomad AFR AF: 0.951

Gnomad AMI AF: 0.910

Gnomad AMR AF: 0.760

Gnomad ASJ AF: 0.886

Gnomad EAS AF: 0.678

Gnomad SAS AF: 0.846

Gnomad FIN AF: 0.831

Gnomad MID AF: 0.943

Gnomad NFE AF: 0.840

Gnomad OTH AF: 0.863

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

GnomAD4 genome AF: 0.858 AC: 130743 AN: 152306 Hom.: 56534 Cov.: 34 AF XY: 0.856 AC XY: 63728 AN XY: 74466

African (AFR) AF: 0.951 AC: 39547 AN: 41584

American (AMR) AF: 0.759 AC: 11620 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.886 AC: 3075 AN: 3472

East Asian (EAS) AF: 0.677 AC: 3511 AN: 5184

South Asian (SAS) AF: 0.845 AC: 4079 AN: 4828

European-Finnish (FIN) AF: 0.831 AC: 8807 AN: 10592

Middle Eastern (MID) AF: 0.932 AC: 274 AN: 294

European-Non Finnish (NFE) AF: 0.840 AC: 57177 AN: 68028

Other (OTH) AF: 0.863 AC: 1823 AN: 2112

Alfa AF: 0.843 Hom.: 225071

Bravo AF: 0.855

Asia WGS AF: 0.778 AC: 2704 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	3.0
DANN	Benign	0.50
PhyloP100		0.28
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: rs3789080; hg19: chr2-111797531;