17-8096271-T-G

Position:

• chr17-8096271-T-G

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_021628.3(ALOXE3):​c.*356A>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.438 in 227,746 control chromosomes in the GnomAD database, including 23,041 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.44 (15249 hom., cov: 31)
  • Exomes 𝑓: 0.44 (7792 hom.)
• Consequence: ALOXE3 NM_021628.3 3_prime_UTR
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -3.18

Genes affected

ALOXE3 (HGNC:13743): (arachidonate lipoxygenase 3) This gene is a member of the lipoxygenase family, which are catabolized by arachidonic acid-derived compounds. The encoded enzyme is a hydroperoxide isomerase that synthesizes a unique type of epoxy alcohol (8R-hydroxy-11R,12R-epoxyeicosa-5Z,9E,14Z-trienoic acid) from 12R-hydroperoxyeicosatetraenoic acid (12R-HPETE). This epoxy alcohol can activate the the nuclear receptor peroxisome proliferator-activated receptor alpha (PPARalpha), which is implicated in epidermal differentiation. Loss of function of the enzyme encoded by this gene results in ichthyosis, implicating the function of this gene in the differentiation of human skin. This gene is part of a cluster of lipoxygenase genes on 17p13.1. Mutations in this gene result in nonbullous congenital ichthyosiform erythroderma (NCIE). Multiple transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Sep 2009]

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BP6: Variant 17-8096271-T-G is Benign according to our data. Variant chr17-8096271-T-G is described in ClinVar as [Benign]. Clinvar id is 325949.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.643 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ALOXE3	NM_021628.3	c.*356A>C		3_prime_UTR_variant	16/16	ENST00000448843.7
ALOXE3	NM_001165960.1	c.*356A>C		3_prime_UTR_variant	16/16
ALOXE3	NM_001369446.1	c.*356A>C		3_prime_UTR_variant	15/15

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ALOXE3	ENST00000448843.7	c.*356A>C		3_prime_UTR_variant	16/16	1	NM_021628.3	P1
ALOXE3	ENST00000380149.6	c.*356A>C		3_prime_UTR_variant	15/15	1		P1
ALOXE3	ENST00000583808.1	n.729A>C		non_coding_transcript_exon_variant	2/2	4

Frequencies

GnomAD3 genomes AF: 0.439 AC: 66540 AN: 151744 Hom.: 15221 Cov.: 31

Gnomad AFR AF: 0.328

Gnomad AMI AF: 0.354

Gnomad AMR AF: 0.566

Gnomad ASJ AF: 0.431

Gnomad EAS AF: 0.661

Gnomad SAS AF: 0.564

Gnomad FIN AF: 0.562

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.434

Gnomad OTH AF: 0.437

GnomAD4 exome AF: 0.435 AC: 33041 AN: 75884 Hom.: 7792 Cov.: 0 AF XY: 0.444 AC XY: 17615 AN XY: 39634

Gnomad4 AFR exome AF: 0.263

Gnomad4 AMR exome AF: 0.592

Gnomad4 ASJ exome AF: 0.387

Gnomad4 EAS exome AF: 0.628

Gnomad4 SAS exome AF: 0.552

Gnomad4 FIN exome AF: 0.491

Gnomad4 NFE exome AF: 0.394

Gnomad4 OTH exome AF: 0.417

GnomAD4 genome AF: 0.439 AC: 66618 AN: 151862 Hom.: 15249 Cov.: 31 AF XY: 0.450 AC XY: 33409 AN XY: 74230

Gnomad4 AFR AF: 0.328

Gnomad4 AMR AF: 0.567

Gnomad4 ASJ AF: 0.431

Gnomad4 EAS AF: 0.662

Gnomad4 SAS AF: 0.564

Gnomad4 FIN AF: 0.562

Gnomad4 NFE AF: 0.434

Gnomad4 OTH AF: 0.441

Alfa AF: 0.435 Hom.: 19843

Bravo AF: 0.434

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Autosomal recessive congenital ichthyosis 3 Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jan 13, 2018

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

not provided Benign:1

Benign, criteria provided, single submitter

not provided

Breakthrough Genomics, Breakthrough Genomics

-

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.082
DANN	Benign	0.48

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: rs3809882; hg19: chr17-7999589;