rs6706577

chr2-111039256-A-Gchr2-111039256-A-T

Variant summary

Our verdict is Benign. Variant got -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

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 -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ACOXL	NM_001142807.4	c.1369+7542A>G		intron_variant		ENST00000439055.6
LOC124907866	XR_007087182.1	n.118-2334T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ACOXL	ENST00000439055.6	c.1369+7542A>G		intron_variant		2	NM_001142807.4
MIR4435-2HG	ENST00000645030.2	n.453-2334T>C		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.596

Gnomad4 AMR AF: 0.465

Gnomad4 ASJ AF: 0.490

Gnomad4 EAS AF: 0.395

Gnomad4 SAS AF: 0.527

Gnomad4 FIN AF: 0.552

Gnomad4 NFE AF: 0.518

Gnomad4 OTH AF: 0.528

Alfa AF: 0.506 Hom.: 37108

Bravo AF: 0.526

Asia WGS AF: 0.468 AC: 1628 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.25
Cadd	Benign	17
Dann	Benign	0.80

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: rs6706577; hg19: chr2-111796833;