rs7602030

chr2-111037932-C-T

Variant summary

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

The NM_001142807.4(ACOXL):c.1369+6218C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.273 in 152,126 control chromosomes in the GnomAD database, including 5,908 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 0.27 (5908 hom., cov: 32)
• Consequence: ACOXL NM_001142807.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.545

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.311 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ACOXL	NM_001142807.4	c.1369+6218C>T		intron_variant		ENST00000439055.6
LOC124907866	XR_007087182.1	n.118-1010G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ACOXL	ENST00000439055.6	c.1369+6218C>T		intron_variant		2	NM_001142807.4
MIR4435-2HG	ENST00000645030.2	n.453-1010G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.273 AC: 41498 AN: 152008 Hom.: 5910 Cov.: 32

Gnomad AFR AF: 0.229

Gnomad AMI AF: 0.330

Gnomad AMR AF: 0.213

Gnomad ASJ AF: 0.317

Gnomad EAS AF: 0.122

Gnomad SAS AF: 0.231

Gnomad FIN AF: 0.331

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.315

Gnomad OTH AF: 0.287

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

GnomAD4 genome AF: 0.273 AC: 41501 AN: 152126 Hom.: 5908 Cov.: 32 AF XY: 0.271 AC XY: 20189 AN XY: 74372

Gnomad4 AFR AF: 0.229

Gnomad4 AMR AF: 0.213

Gnomad4 ASJ AF: 0.317

Gnomad4 EAS AF: 0.122

Gnomad4 SAS AF: 0.233

Gnomad4 FIN AF: 0.331

Gnomad4 NFE AF: 0.315

Gnomad4 OTH AF: 0.286

Alfa AF: 0.307 Hom.: 14967

Bravo AF: 0.259

Asia WGS AF: 0.170 AC: 591 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	0.090
Dann	Benign	0.59

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: rs7602030; hg19: chr2-111795509;