rs9904779

Positions:

• chr17-6995296-C-G
• chr17-6995296-C-T

Variant summary

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

The NR_040089.1(ALOX12-AS1):​n.234-9756G>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 0.558 in 152,072 control chromosomes in the GnomAD database, including 24,304 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 0.56 (24282 hom., cov: 32)
  • Exomes 𝑓: 0.67 (22 hom.)
• Consequence: ALOX12-AS1 NR_040089.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.448

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=-0.84).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.648 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ALOX12-AS1	NR_040089.1	n.234-9756G>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+16900G>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.558 AC: 84763 AN: 151862 Hom.: 24264 Cov.: 32

Gnomad AFR AF: 0.423

Gnomad AMI AF: 0.615

Gnomad AMR AF: 0.659

Gnomad ASJ AF: 0.576

Gnomad EAS AF: 0.521

Gnomad SAS AF: 0.541

Gnomad FIN AF: 0.655

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.605

Gnomad OTH AF: 0.562

GnomAD4 exome AF: 0.674 AC: 62 AN: 92 Hom.: 22 AF XY: 0.720 AC XY: 36 AN XY: 50

Gnomad4 AFR exome AF: 0.750

Gnomad4 ASJ exome AF: 0.500

Gnomad4 EAS exome AF: 0.600

Gnomad4 FIN exome AF: 0.800

Gnomad4 NFE exome AF: 0.667

Gnomad4 OTH exome AF: 0.667

GnomAD4 genome AF: 0.558 AC: 84818 AN: 151980 Hom.: 24282 Cov.: 32 AF XY: 0.562 AC XY: 41728 AN XY: 74282

Gnomad4 AFR AF: 0.423

Gnomad4 AMR AF: 0.659

Gnomad4 ASJ AF: 0.576

Gnomad4 EAS AF: 0.521

Gnomad4 SAS AF: 0.541

Gnomad4 FIN AF: 0.655

Gnomad4 NFE AF: 0.605

Gnomad4 OTH AF: 0.562

Alfa AF: 0.484 Hom.: 1513

Bravo AF: 0.552

Asia WGS AF: 0.536 AC: 1866 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.7
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9904779; hg19: chr17-6898615; COSMIC: COSV52349082;