rs6503075

chr17-8075433-G-A

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_001139.3(ALOX12B):c.1654+162C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.476 in 151,966 control chromosomes in the GnomAD database, including 17,289 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.48 (17289 hom., cov: 32)
• Consequence: ALOX12B NM_001139.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.0570

Genes affected

ALOX12B (HGNC:430): (arachidonate 12-lipoxygenase, 12R type) This gene encodes an enzyme involved in the conversion of arachidonic acid to 12R-hydroxyeicosatetraenoic acid. Mutations in this gene are associated with nonbullous congenital ichthyosiform erythroderma. [provided by RefSeq, Sep 2015]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BP6: Variant 17-8075433-G-A is Benign according to our data. Variant chr17-8075433-G-A is described in ClinVar as [Benign]. Clinvar id is 1281047.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.539 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ALOX12B	NM_001139.3	c.1654+162C>T		intron_variant		ENST00000647874.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ALOX12B	ENST00000647874.1	c.1654+162C>T		intron_variant			NM_001139.3	P1
ALOX12B	ENST00000649809.1	c.718+162C>T		intron_variant
ALOX12B	ENST00000577351.5	n.479+742C>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.476 AC: 72265 AN: 151848 Hom.: 17282 Cov.: 32

Gnomad AFR AF: 0.483

Gnomad AMI AF: 0.485

Gnomad AMR AF: 0.412

Gnomad ASJ AF: 0.467

Gnomad EAS AF: 0.326

Gnomad SAS AF: 0.555

Gnomad FIN AF: 0.438

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.499

Gnomad OTH AF: 0.462

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

GnomAD4 genome AF: 0.476 AC: 72307 AN: 151966 Hom.: 17289 Cov.: 32 AF XY: 0.474 AC XY: 35204 AN XY: 74288

Gnomad4 AFR AF: 0.483

Gnomad4 AMR AF: 0.411

Gnomad4 ASJ AF: 0.467

Gnomad4 EAS AF: 0.326

Gnomad4 SAS AF: 0.557

Gnomad4 FIN AF: 0.438

Gnomad4 NFE AF: 0.499

Gnomad4 OTH AF: 0.457

Alfa AF: 0.494 Hom.: 9876

Bravo AF: 0.470

Asia WGS AF: 0.397 AC: 1386 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 10, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	5.0
Dann	Benign	0.67

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: rs6503075; hg19: chr17-7978751; COSMIC: COSV59874436; COSMIC: COSV59874436;