rs2289321

Variant names:

• chr2-111112643-T-C
• rs2289321
• NM_001142807.4:c.1543-4973T>C

Your query was ambiguous. Multiple possible variants found:

• chr2-111112643-T-C
• chr2-111112643-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001142807.4(ACOXL):​c.1543-4973T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0767 in 152,248 control chromosomes in the GnomAD database, including 552 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 0.077 (552 hom., cov: 33)
• Consequence: ACOXL NM_001142807.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.51

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]

ACOXL-AS1 (HGNC:41112): (ACOXL antisense RNA 1)

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.119 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ACOXL	NM_001142807.4	c.1543-4973T>C		intron_variant	Intron 17 of 17	ENST00000439055.6	NP_001136279.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ACOXL	ENST00000439055.6	c.1543-4973T>C		intron_variant	Intron 17 of 17	2	NM_001142807.4	ENSP00000407761.1

Frequencies

GnomAD3 genomes AF: 0.0767 AC: 11663 AN: 152130 Hom.: 550 Cov.: 33

Gnomad AFR AF: 0.107

Gnomad AMI AF: 0.115

Gnomad AMR AF: 0.0866

Gnomad ASJ AF: 0.0340

Gnomad EAS AF: 0.126

Gnomad SAS AF: 0.0725

Gnomad FIN AF: 0.0367

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0604

Gnomad OTH AF: 0.0827

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

GnomAD4 genome AF: 0.0767 AC: 11677 AN: 152248 Hom.: 552 Cov.: 33 AF XY: 0.0780 AC XY: 5808 AN XY: 74448

Gnomad4 AFR AF: 0.107

Gnomad4 AMR AF: 0.0865

Gnomad4 ASJ AF: 0.0340

Gnomad4 EAS AF: 0.127

Gnomad4 SAS AF: 0.0728

Gnomad4 FIN AF: 0.0367

Gnomad4 NFE AF: 0.0604

Gnomad4 OTH AF: 0.0814

Alfa AF: 0.0634 Hom.: 478

Bravo AF: 0.0814

Asia WGS AF: 0.0750 AC: 261 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.90
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2289321; hg19: chr2-111870220;