rs6502998

Positions:

• chr17-6986238-G-A
• chr17-6986238-G-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.234-698C>T 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 0.679 in 151,840 control chromosomes in the GnomAD database, including 35,943 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 0.68 (35943 hom., cov: 31)
• Consequence: ALOX12-AS1 NR_040089.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.140

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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.833 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ALOX12-AS1	NR_040089.1	n.234-698C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ALOX12-AS1	ENST00000653385.1	n.139+25958C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.679 AC: 102957 AN: 151722 Hom.: 35882 Cov.: 31

Gnomad AFR AF: 0.840

Gnomad AMI AF: 0.599

Gnomad AMR AF: 0.742

Gnomad ASJ AF: 0.579

Gnomad EAS AF: 0.608

Gnomad SAS AF: 0.546

Gnomad FIN AF: 0.651

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.593

Gnomad OTH AF: 0.656

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

GnomAD4 genome AF: 0.679 AC: 103073 AN: 151840 Hom.: 35943 Cov.: 31 AF XY: 0.679 AC XY: 50402 AN XY: 74190

Gnomad4 AFR AF: 0.840

Gnomad4 AMR AF: 0.742

Gnomad4 ASJ AF: 0.579

Gnomad4 EAS AF: 0.607

Gnomad4 SAS AF: 0.546

Gnomad4 FIN AF: 0.651

Gnomad4 NFE AF: 0.593

Gnomad4 OTH AF: 0.655

Alfa AF: 0.613 Hom.: 21590

Bravo AF: 0.694

Asia WGS AF: 0.610 AC: 2124 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.5
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6502998; hg19: chr17-6889557;