17-7012082-C-G

Variant summary

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

The NR_040089.1(ALOX12-AS1):n.139+114G>C 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 0.601 in 392,134 control chromosomes in the GnomAD database, including 72,031 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 0.58 (26029 hom., cov: 32)
  • Exomes 𝑓: 0.61 (46002 hom.)
• Consequence: ALOX12-AS1 NR_040089.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.21

Genes affected

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=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.71 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ALOX12-AS1	NR_040089.1	n.139+114G>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ALOX12-AS1	ENST00000653385.1	n.139+114G>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.583 AC: 88625 AN: 151886 Hom.: 26009 Cov.: 32

Gnomad AFR AF: 0.547

Gnomad AMI AF: 0.638

Gnomad AMR AF: 0.527

Gnomad ASJ AF: 0.634

Gnomad EAS AF: 0.551

Gnomad SAS AF: 0.730

Gnomad FIN AF: 0.563

Gnomad MID AF: 0.672

Gnomad NFE AF: 0.610

Gnomad OTH AF: 0.602

GnomAD4 exome AF: 0.612 AC: 147048 AN: 240130 Hom.: 46002 AF XY: 0.626 AC XY: 84245 AN XY: 134498

Gnomad4 AFR exome AF: 0.533

Gnomad4 AMR exome AF: 0.446

Gnomad4 ASJ exome AF: 0.630

Gnomad4 EAS exome AF: 0.532

Gnomad4 SAS exome AF: 0.728

Gnomad4 FIN exome AF: 0.584

Gnomad4 NFE exome AF: 0.603

Gnomad4 OTH exome AF: 0.605

GnomAD4 genome AF: 0.583 AC: 88694 AN: 152004 Hom.: 26029 Cov.: 32 AF XY: 0.583 AC XY: 43345 AN XY: 74298

Gnomad4 AFR AF: 0.547

Gnomad4 AMR AF: 0.526

Gnomad4 ASJ AF: 0.634

Gnomad4 EAS AF: 0.552

Gnomad4 SAS AF: 0.730

Gnomad4 FIN AF: 0.563

Gnomad4 NFE AF: 0.610

Gnomad4 OTH AF: 0.600

Alfa AF: 0.461 Hom.: 1238

Bravo AF: 0.573

Asia WGS AF: 0.613 AC: 2138 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	0.095
Dann	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2271316; hg19: chr17-6915401;