rs7567444

Variant names:

• chr2-111105861-T-C
• rs7567444
• NM_001142807.4:c.1543-11755T>C

Your query was ambiguous. Multiple possible variants found:

• chr2-111105861-T-C
• chr2-111105861-T-G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001142807.4(ACOXL):​c.1543-11755T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.581 in 151,966 control chromosomes in the GnomAD database, including 27,146 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 0.58 (27146 hom., cov: 32)
• Consequence: ACOXL NM_001142807.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0330
• Publications: 11 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]

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

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.768 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ACOXL	NM_001142807.4	MANE Select	c.1543-11755T>C		intron	N/A	NP_001136279.1	Q9NUZ1-4
	ACOXL	NM_001437600.1		c.1633-11755T>C		intron	N/A	NP_001424529.1	A0A7I2V3X2
	ACOXL-AS1	NR_122074.1		n.230-3785A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ACOXL	ENST00000439055.6	TSL:2 MANE Select	c.1543-11755T>C		intron	N/A	ENSP00000407761.1	Q9NUZ1-4
	ACOXL	ENST00000957119.1		c.1675-11755T>C		intron	N/A	ENSP00000627178.1
	ACOXL	ENST00000957116.1		c.1660-11755T>C		intron	N/A	ENSP00000627175.1

Frequencies

GnomAD3 genomes AF: 0.581 AC: 88170 AN: 151848 Hom.: 27101 Cov.: 32

Gnomad AFR AF: 0.775

Gnomad AMI AF: 0.562

Gnomad AMR AF: 0.402

Gnomad ASJ AF: 0.413

Gnomad EAS AF: 0.558

Gnomad SAS AF: 0.313

Gnomad FIN AF: 0.545

Gnomad MID AF: 0.350

Gnomad NFE AF: 0.540

Gnomad OTH AF: 0.536

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

GnomAD4 genome AF: 0.581 AC: 88265 AN: 151966 Hom.: 27146 Cov.: 32 AF XY: 0.573 AC XY: 42536 AN XY: 74282

African (AFR) AF: 0.776 AC: 32161 AN: 41470

American (AMR) AF: 0.401 AC: 6130 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.413 AC: 1432 AN: 3468

East Asian (EAS) AF: 0.558 AC: 2881 AN: 5160

South Asian (SAS) AF: 0.313 AC: 1507 AN: 4816

European-Finnish (FIN) AF: 0.545 AC: 5747 AN: 10548

Middle Eastern (MID) AF: 0.349 AC: 102 AN: 292

European-Non Finnish (NFE) AF: 0.540 AC: 36670 AN: 67926

Other (OTH) AF: 0.535 AC: 1126 AN: 2104

Alfa AF: 0.526 Hom.: 26391

Bravo AF: 0.584

Asia WGS AF: 0.428 AC: 1489 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.2
DANN	Benign	0.75
PhyloP100		-0.033
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs7567444; hg19: chr2-111863438;