2-111116699-C-T

Position:

• chr2-111116699-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.1543-917C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.428 in 151,722 control chromosomes in the GnomAD database, including 14,369 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 0.43 (14369 hom., cov: 32)
• Consequence: ACOXL NM_001142807.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.298

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=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.473 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ACOXL	NM_001142807.4	c.1543-917C>T		intron_variant		ENST00000439055.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ACOXL	ENST00000439055.6	c.1543-917C>T		intron_variant		2	NM_001142807.4
MIR4435-2HG	ENST00000645030.2	n.453-79777G>A		intron_variant, non_coding_transcript_variant
ACOXL	ENST00000441974.1	c.*41-917C>T		intron_variant		5
ACOXL	ENST00000676595.2	c.1633-917C>T		intron_variant				P1

Frequencies

GnomAD3 genomes AF: 0.428 AC: 64888 AN: 151604 Hom.: 14367 Cov.: 32

Gnomad AFR AF: 0.408

Gnomad AMI AF: 0.444

Gnomad AMR AF: 0.292

Gnomad ASJ AF: 0.369

Gnomad EAS AF: 0.431

Gnomad SAS AF: 0.226

Gnomad FIN AF: 0.509

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.477

Gnomad OTH AF: 0.393

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

GnomAD4 genome AF: 0.428 AC: 64910 AN: 151722 Hom.: 14369 Cov.: 32 AF XY: 0.422 AC XY: 31276 AN XY: 74096

Gnomad4 AFR AF: 0.408

Gnomad4 AMR AF: 0.291

Gnomad4 ASJ AF: 0.369

Gnomad4 EAS AF: 0.430

Gnomad4 SAS AF: 0.226

Gnomad4 FIN AF: 0.509

Gnomad4 NFE AF: 0.477

Gnomad4 OTH AF: 0.394

Alfa AF: 0.443 Hom.: 7879

Bravo AF: 0.415

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	1.5
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1837369; hg19: chr2-111874276;