chr2-111039256-A-G

Variant names:

• chr2-111039256-A-G
• rs6706577
• NM_001142807.4:c.1369+7542A>G

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_001142807.4(ACOXL):​c.1369+7542A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.532 in 152,090 control chromosomes in the GnomAD database, including 21,839 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 0.53 (21839 hom., cov: 33)
• Consequence: ACOXL NM_001142807.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.536
• Publications: 9 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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.25).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.59 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.1369+7542A>G		intron	N/A	NP_001136279.1
	ACOXL	NM_001437600.1		c.1459+7542A>G		intron	N/A	NP_001424529.1
	ACOXL	NM_001371254.1		c.1459+7542A>G		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.1369+7542A>G		intron	N/A	ENSP00000407761.1
	ACOXL	ENST00000417074.5	TSL:1	c.883+7542A>G		intron	N/A	ENSP00000387832.1
	ACOXL	ENST00000676595.2		c.1459+7542A>G		intron	N/A	ENSP00000503683.1

Frequencies

GnomAD3 genomes AF: 0.532 AC: 80823 AN: 151972 Hom.: 21822 Cov.: 33

Gnomad AFR AF: 0.596

Gnomad AMI AF: 0.504

Gnomad AMR AF: 0.466

Gnomad ASJ AF: 0.490

Gnomad EAS AF: 0.395

Gnomad SAS AF: 0.527

Gnomad FIN AF: 0.552

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.518

Gnomad OTH AF: 0.527

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

GnomAD4 genome AF: 0.532 AC: 80889 AN: 152090 Hom.: 21839 Cov.: 33 AF XY: 0.531 AC XY: 39466 AN XY: 74336

African (AFR) AF: 0.596 AC: 24730 AN: 41490

American (AMR) AF: 0.465 AC: 7102 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.490 AC: 1702 AN: 3472

East Asian (EAS) AF: 0.395 AC: 2050 AN: 5190

South Asian (SAS) AF: 0.527 AC: 2544 AN: 4828

European-Finnish (FIN) AF: 0.552 AC: 5826 AN: 10562

Middle Eastern (MID) AF: 0.514 AC: 151 AN: 294

European-Non Finnish (NFE) AF: 0.518 AC: 35212 AN: 67958

Other (OTH) AF: 0.528 AC: 1114 AN: 2110

Alfa AF: 0.514 Hom.: 81591

Bravo AF: 0.526

Asia WGS AF: 0.468 AC: 1628 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.25
CADD	Benign	17
DANN	Benign	0.80
PhyloP100		0.54
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: rs6706577; hg19: chr2-111796833;