rs58630086

Positions:

• chr17-6878094-G-A
• chr17-6878094-G-C

Variant summary

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

The NR_002710.2(ALOX12P2):​n.708-13909G>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 0.0539 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 NR_002710.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.171

Genes affected

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

ALOX12-AS1 (HGNC:51342): (ALOX12 antisense RNA 1)

LOC124903907 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ALOX12P2	NR_002710.2	n.708-13909G>A		intron_variant, non_coding_transcript_variant
LOC124903907	XR_007065596.1	n.6069-1207C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ALOX12-AS1	ENST00000653385.1	n.293-1207C>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.0613

Gnomad4 AMR AF: 0.0722

Gnomad4 ASJ AF: 0.0156

Gnomad4 EAS AF: 0.215

Gnomad4 SAS AF: 0.0232

Gnomad4 FIN AF: 0.0324

Gnomad4 NFE AF: 0.0416

Gnomad4 OTH AF: 0.0455

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs58630086; hg19: chr17-6781413;