chr17-8087771-C-T

Variant names:

• chr17-8087771-C-T
• rs3027309
• NM_001139.3:c.-329G>A

Variant summary

Our verdict is Benign. Variant got -18 ACMG points: 0P and 18B. BP4_Moderate BP6_Very_Strong BA1

The NM_001139.3(ALOX12B):​c.-329G>A variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.177 in 472,870 control chromosomes in the GnomAD database, including 8,043 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.15 (2059 hom., cov: 32)
  • Exomes 𝑓: 0.19 (5984 hom.)
• Consequence: ALOX12B NM_001139.3 upstream_gene
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: 0.121

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 -18 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.27).
• BP6: Variant 17-8087771-C-T is Benign according to our data. Variant chr17-8087771-C-T is described in ClinVar as [Benign]. Clinvar id is 1271783.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.21 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ALOX12B	NM_001139.3	c.-329G>A		upstream_gene_variant		ENST00000647874.1	NP_001130.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ALOX12B	ENST00000647874.1	c.-329G>A		upstream_gene_variant			NM_001139.3	ENSP00000497784.1

Frequencies

GnomAD3 genomes AF: 0.154 AC: 23380 AN: 151948 Hom.: 2053 Cov.: 32

Gnomad AFR AF: 0.0733

Gnomad AMI AF: 0.117

Gnomad AMR AF: 0.191

Gnomad ASJ AF: 0.112

Gnomad EAS AF: 0.147

Gnomad SAS AF: 0.220

Gnomad FIN AF: 0.176

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.190

Gnomad OTH AF: 0.151

GnomAD4 exome AF: 0.188 AC: 60224 AN: 320804 Hom.: 5984 AF XY: 0.191 AC XY: 31878 AN XY: 166854

Gnomad4 AFR exome AF: 0.0733

Gnomad4 AMR exome AF: 0.190

Gnomad4 ASJ exome AF: 0.106

Gnomad4 EAS exome AF: 0.165

Gnomad4 SAS exome AF: 0.234

Gnomad4 FIN exome AF: 0.184

Gnomad4 NFE exome AF: 0.193

Gnomad4 OTH exome AF: 0.173

GnomAD4 genome AF: 0.154 AC: 23408 AN: 152066 Hom.: 2059 Cov.: 32 AF XY: 0.156 AC XY: 11558 AN XY: 74320

Gnomad4 AFR AF: 0.0735

Gnomad4 AMR AF: 0.191

Gnomad4 ASJ AF: 0.112

Gnomad4 EAS AF: 0.147

Gnomad4 SAS AF: 0.221

Gnomad4 FIN AF: 0.176

Gnomad4 NFE AF: 0.190

Gnomad4 OTH AF: 0.156

Alfa AF: 0.0855 Hom.: 192

Bravo AF: 0.150

Asia WGS AF: 0.176 AC: 614 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

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Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Jun 18, 2021

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.27
CADD	Benign	16
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3027309; hg19: chr17-7991089;