rs3840880

Positions:

• chr17-6994524-TC-T

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NR_040089.1(ALOX12-AS1):​n.234-8985del 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 0.562 in 151,982 control chromosomes in the GnomAD database, including 24,355 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.56 (24355 hom., cov: 0)
  • Exomes 𝑓: 0.33 (0 hom.)
• Consequence: ALOX12-AS1 NR_040089.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.105

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.639 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ALOX12-AS1	NR_040089.1	n.234-8985del		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ALOX12-AS1	ENST00000653385.1	n.139+17671del		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.562 AC: 85301 AN: 151858 Hom.: 24331 Cov.: 0

Gnomad AFR AF: 0.470

Gnomad AMI AF: 0.613

Gnomad AMR AF: 0.649

Gnomad ASJ AF: 0.538

Gnomad EAS AF: 0.587

Gnomad SAS AF: 0.534

Gnomad FIN AF: 0.649

Gnomad MID AF: 0.545

Gnomad NFE AF: 0.585

Gnomad OTH AF: 0.563

GnomAD4 exome AF: 0.333 AC: 2 AN: 6 Hom.: 0 AF XY: 0.500 AC XY: 2 AN XY: 4

Gnomad4 NFE exome AF: 0.333

GnomAD4 genome AF: 0.562 AC: 85374 AN: 151976 Hom.: 24355 Cov.: 0 AF XY: 0.566 AC XY: 42042 AN XY: 74288

Gnomad4 AFR AF: 0.471

Gnomad4 AMR AF: 0.650

Gnomad4 ASJ AF: 0.538

Gnomad4 EAS AF: 0.587

Gnomad4 SAS AF: 0.534

Gnomad4 FIN AF: 0.649

Gnomad4 NFE AF: 0.585

Gnomad4 OTH AF: 0.563

Alfa AF: 0.365 Hom.: 1218

Bravo AF: 0.557

Asia WGS AF: 0.550 AC: 1918 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3840880; hg19: chr17-6897843;