rs6502997

chr17-6984439-A-Cchr17-6984439-A-T

Variant summary

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

The ENST00000653385.1(ALOX12-AS1):n.139+27757T>G 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 0.653 in 152,008 control chromosomes in the GnomAD database, including 32,663 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 0.65 (32663 hom., cov: 33)
• Consequence: ALOX12-AS1 ENST00000653385.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.50

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=-0.74).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.69 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ALOX12-AS1	ENST00000653385.1	n.139+27757T>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.654 AC: 99269 AN: 151890 Hom.: 32640 Cov.: 33

Gnomad AFR AF: 0.698

Gnomad AMI AF: 0.600

Gnomad AMR AF: 0.538

Gnomad ASJ AF: 0.702

Gnomad EAS AF: 0.696

Gnomad SAS AF: 0.662

Gnomad FIN AF: 0.592

Gnomad MID AF: 0.753

Gnomad NFE AF: 0.656

Gnomad OTH AF: 0.663

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

GnomAD4 genome AF: 0.653 AC: 99332 AN: 152008 Hom.: 32663 Cov.: 33 AF XY: 0.649 AC XY: 48202 AN XY: 74306

Gnomad4 AFR AF: 0.697

Gnomad4 AMR AF: 0.537

Gnomad4 ASJ AF: 0.702

Gnomad4 EAS AF: 0.697

Gnomad4 SAS AF: 0.664

Gnomad4 FIN AF: 0.592

Gnomad4 NFE AF: 0.656

Gnomad4 OTH AF: 0.667

Alfa AF: 0.634 Hom.: 14517

Bravo AF: 0.646

Asia WGS AF: 0.660 AC: 2300 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
Cadd	Benign	6.1
Dann	Benign	0.95

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6502997; hg19: chr17-6887758;