rs7220870

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000574640.1(ALOX15):​c.-272G>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.219 in 533,576 control chromosomes in the GnomAD database, including 13,483 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 0.20 ( 3301 hom., cov: 31)
Exomes 𝑓: 0.23 ( 10182 hom. )

Consequence

ALOX15
ENST00000574640.1 5_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.886
Variant links:
Genes affected
ALOX15 (HGNC:433): (arachidonate 15-lipoxygenase) This gene encodes a member of the lipoxygenase family of proteins. The encoded enzyme acts on various polyunsaturated fatty acid substrates to generate various bioactive lipid mediators such as eicosanoids, hepoxilins, lipoxins, and other molecules. The encoded enzyme and its reaction products have been shown to regulate inflammation and immunity. Multiple pseudogenes of this gene have been identified in the human genome. [provided by RefSeq, Aug 2017]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.31 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ALOX15ENST00000574640.1 linkuse as main transcriptc.-272G>T 5_prime_UTR_variant 1/142 ENSP00000460483 P16050-2
ALOX15ENST00000570836.6 linkuse as main transcriptc.-25-247G>T intron_variant 2 ENSP00000458832 P1P16050-1

Frequencies

GnomAD3 genomes
AF:
0.204
AC:
30940
AN:
151782
Hom.:
3296
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.151
Gnomad AMI
AF:
0.130
Gnomad AMR
AF:
0.226
Gnomad ASJ
AF:
0.255
Gnomad EAS
AF:
0.175
Gnomad SAS
AF:
0.324
Gnomad FIN
AF:
0.238
Gnomad MID
AF:
0.226
Gnomad NFE
AF:
0.218
Gnomad OTH
AF:
0.211
GnomAD4 exome
AF:
0.225
AC:
85966
AN:
381676
Hom.:
10182
Cov.:
4
AF XY:
0.231
AC XY:
46411
AN XY:
201298
show subpopulations
Gnomad4 AFR exome
AF:
0.158
Gnomad4 AMR exome
AF:
0.243
Gnomad4 ASJ exome
AF:
0.273
Gnomad4 EAS exome
AF:
0.147
Gnomad4 SAS exome
AF:
0.309
Gnomad4 FIN exome
AF:
0.226
Gnomad4 NFE exome
AF:
0.217
Gnomad4 OTH exome
AF:
0.226
GnomAD4 genome
AF:
0.204
AC:
30969
AN:
151900
Hom.:
3301
Cov.:
31
AF XY:
0.206
AC XY:
15260
AN XY:
74208
show subpopulations
Gnomad4 AFR
AF:
0.151
Gnomad4 AMR
AF:
0.226
Gnomad4 ASJ
AF:
0.255
Gnomad4 EAS
AF:
0.176
Gnomad4 SAS
AF:
0.323
Gnomad4 FIN
AF:
0.238
Gnomad4 NFE
AF:
0.218
Gnomad4 OTH
AF:
0.210
Alfa
AF:
0.157
Hom.:
549
Bravo
AF:
0.202
Asia WGS
AF:
0.253
AC:
880
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.88
CADD
Benign
1.6
DANN
Benign
0.69

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.030
Details are displayed if max score is > 0.2

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.

Other links and lift over

dbSNP: rs7220870; hg19: chr17-4545218; API