17-6878094-G-A

Variant names:

• chr17-6878094-G-A
• rs58630086
• ENST00000574727.5:n.423-13909G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000574727.5(ALOX12P2):​n.423-13909G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0539 in 152,112 control chromosomes in the GnomAD database, including 346 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 0.054 (346 hom., cov: 32)
• Consequence: ALOX12P2 ENST00000574727.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.171
• Publications: 3 publications found

Genes affected

ALOX12P2 (HGNC:):

MIR497HG (HGNC:39523): (mir-497-195 cluster host gene)

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.205 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000574727.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ALOX12P2	NR_002710.2		n.708-13909G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ALOX12P2	ENST00000574727.5	TSL:1	n.423-13909G>A		intron	N/A
	MIR497HG	ENST00000570562.5	TSL:3	n.391-1207C>T		intron	N/A
	ALOX12P2	ENST00000570835.1	TSL:4	n.359-13913G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0539 AC: 8199 AN: 151992 Hom.: 347 Cov.: 32

Gnomad AFR AF: 0.0614

Gnomad AMI AF: 0.00548

Gnomad AMR AF: 0.0723

Gnomad ASJ AF: 0.0156

Gnomad EAS AF: 0.215

Gnomad SAS AF: 0.0226

Gnomad FIN AF: 0.0324

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0416

Gnomad OTH AF: 0.0460

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

GnomAD4 genome AF: 0.0539 AC: 8205 AN: 152112 Hom.: 346 Cov.: 32 AF XY: 0.0531 AC XY: 3948 AN XY: 74346

African (AFR) AF: 0.0613 AC: 2544 AN: 41490

American (AMR) AF: 0.0722 AC: 1104 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0156 AC: 54 AN: 3464

East Asian (EAS) AF: 0.215 AC: 1113 AN: 5172

South Asian (SAS) AF: 0.0232 AC: 112 AN: 4822

European-Finnish (FIN) AF: 0.0324 AC: 343 AN: 10578

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.0416 AC: 2829 AN: 67980

Other (OTH) AF: 0.0455 AC: 96 AN: 2110

Alfa AF: 0.00638 Hom.: 1

Bravo AF: 0.0602

Asia WGS AF: 0.0910 AC: 316 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	11
DANN	Benign	0.91
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs58630086; hg19: chr17-6781413;