17-30529657-T-G

Variant names:

• chr17-30529657-T-G
• rs216465
• ENST00000579299.2:n.-31T>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000579299.2(ALOX12P1):​n.-31T>G variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.429 in 152,420 control chromosomes in the GnomAD database, including 14,833 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 (14807 hom., cov: 32)
  • Exomes 𝑓: 0.38 (26 hom.)
• Consequence: ALOX12P1 ENST00000579299.2 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0760

Genes affected

ALOX12P1 (HGNC:431): (arachidonate 12-lipoxygenase pseudogene 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.816 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ALOX12P1	ENST00000579299.2	n.-31T>G		upstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.430 AC: 65226 AN: 151860 Hom.: 14801 Cov.: 32

Gnomad AFR AF: 0.338

Gnomad AMI AF: 0.466

Gnomad AMR AF: 0.484

Gnomad ASJ AF: 0.472

Gnomad EAS AF: 0.836

Gnomad SAS AF: 0.478

Gnomad FIN AF: 0.410

Gnomad MID AF: 0.417

Gnomad NFE AF: 0.438

Gnomad OTH AF: 0.450

GnomAD4 exome AF: 0.375 AC: 165 AN: 440 Hom.: 26 Cov.: 0 AF XY: 0.354 AC XY: 95 AN XY: 268

Gnomad4 FIN exome AF: 0.383

Gnomad4 NFE exome AF: 0.125

Gnomad4 OTH exome AF: 0.250

GnomAD4 genome AF: 0.429 AC: 65247 AN: 151980 Hom.: 14807 Cov.: 32 AF XY: 0.434 AC XY: 32257 AN XY: 74296

Gnomad4 AFR AF: 0.337

Gnomad4 AMR AF: 0.484

Gnomad4 ASJ AF: 0.472

Gnomad4 EAS AF: 0.837

Gnomad4 SAS AF: 0.478

Gnomad4 FIN AF: 0.410

Gnomad4 NFE AF: 0.438

Gnomad4 OTH AF: 0.452

Alfa AF: 0.427 Hom.: 2251

Bravo AF: 0.434

Asia WGS AF: 0.600 AC: 2087 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	9.8
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs216465; hg19: chr17-28856675;