rs10207392

Positions:

• chr2-111092082-A-G

Variant summary

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

The NM_001142807.4(ACOXL):​c.1441-783A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.479 in 152,002 control chromosomes in the GnomAD database, including 17,598 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 0.48 (17598 hom., cov: 32)
• Consequence: ACOXL NM_001142807.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.46

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.535 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ACOXL	NM_001142807.4	c.1441-783A>G		intron_variant		ENST00000439055.6	NP_001136279.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ACOXL	ENST00000439055.6	c.1441-783A>G		intron_variant		2	NM_001142807.4	ENSP00000407761
MIR4435-2HG	ENST00000645030.2	n.453-55160T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.480 AC: 72840 AN: 151884 Hom.: 17588 Cov.: 32

Gnomad AFR AF: 0.541

Gnomad AMI AF: 0.532

Gnomad AMR AF: 0.434

Gnomad ASJ AF: 0.410

Gnomad EAS AF: 0.532

Gnomad SAS AF: 0.474

Gnomad FIN AF: 0.459

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.456

Gnomad OTH AF: 0.460

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

GnomAD4 genome AF: 0.479 AC: 72877 AN: 152002 Hom.: 17598 Cov.: 32 AF XY: 0.478 AC XY: 35480 AN XY: 74276

Gnomad4 AFR AF: 0.541

Gnomad4 AMR AF: 0.433

Gnomad4 ASJ AF: 0.410

Gnomad4 EAS AF: 0.531

Gnomad4 SAS AF: 0.471

Gnomad4 FIN AF: 0.459

Gnomad4 NFE AF: 0.456

Gnomad4 OTH AF: 0.461

Alfa AF: 0.451 Hom.: 31063

Bravo AF: 0.479

Asia WGS AF: 0.491 AC: 1709 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.88
DANN	Benign	0.76

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

Publications

LitVar

Other links and lift over

dbSNP: rs10207392; hg19: chr2-111849659;