Variant rs3840880 details in Genebe, Genetics Data Aggregator

Variant summary

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

The ENST00000399541.6(ALOX12-AS1):n.234-8985delG variant causes a intron 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
ENST00000399541.6 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.105

Variant links:

Genes affected

ALOX12-AS1 (HGNC:):

ALOX12-AS1 links:

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

ALOX12-AS1 links:

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ACMG classification

Classification made for transcript

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	Protein	UniProt
ALOX12-AS1	NR_040089.1 link	n.234-8985delG		intron_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL
ALOX12-AS1	ENST00000399541.6 link	n.234-8985delG	intron_variant	2
ALOX12-AS1	ENST00000570562.5 link	n.237+15271delG	intron_variant	3
ALOX12-AS1	ENST00000572385.5 link	n.230+15271delG	intron_variant	4

Frequencies

GnomAD3 genomes

AF:

0.562

AC:

85301

AN:

151858

Hom.:

24331

Cov.:

show subpopulations

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:

AN:

Hom.:

AF XY:

0.500

AC XY:

AN XY:

show subpopulations

Gnomad4 NFE exome

AF:

0.333

GnomAD4 genome

AF:

0.562

AC:

85374

AN:

151976

Hom.:

24355

Cov.:

AF XY:

0.566

AC XY:

42042

AN XY:

74288

show subpopulations

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

Name

Calibrated prediction

Score

Prediction

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over