rs1696

chr17-6941095-G-A

Variant summary

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

The ENST00000574183.1(ALOX12P2):n.73-12566G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.116 in 152,006 control chromosomes in the GnomAD database, including 1,435 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 0.12 (1435 hom., cov: 31)
• Consequence: ALOX12P2 ENST00000574183.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.598

Genes affected

ALOX12P2 (HGNC:432): (arachidonate 12-lipoxygenase pseudogene 2)

ALOX12-AS1 (HGNC:51342): (ALOX12 antisense RNA 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 (AFR) allele frequency at 95% confidence interval = 0.226 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ALOX12P2	ENST00000574183.1	n.73-12566G>A		intron_variant, non_coding_transcript_variant		3
ALOX12-AS1	ENST00000653385.1	n.140-60033C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.116 AC: 17580 AN: 151888 Hom.: 1426 Cov.: 31

Gnomad AFR AF: 0.230

Gnomad AMI AF: 0.0253

Gnomad AMR AF: 0.0831

Gnomad ASJ AF: 0.125

Gnomad EAS AF: 0.00154

Gnomad SAS AF: 0.0792

Gnomad FIN AF: 0.0560

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.0748

Gnomad OTH AF: 0.110

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

GnomAD4 genome AF: 0.116 AC: 17613 AN: 152006 Hom.: 1435 Cov.: 31 AF XY: 0.112 AC XY: 8344 AN XY: 74304

Gnomad4 AFR AF: 0.230

Gnomad4 AMR AF: 0.0831

Gnomad4 ASJ AF: 0.125

Gnomad4 EAS AF: 0.00154

Gnomad4 SAS AF: 0.0793

Gnomad4 FIN AF: 0.0560

Gnomad4 NFE AF: 0.0749

Gnomad4 OTH AF: 0.109

Alfa AF: 0.0883 Hom.: 434

Bravo AF: 0.122

Asia WGS AF: 0.0480 AC: 167 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	1.6
Dann	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1696; hg19: chr17-6844414;