GeneBe

17-30529657-T-G

Variant names:

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000579299.2(ALOX12P1):​n.-31T>G variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.429 in 152,420 control chromosomes in the GnomAD database, including 14,833 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 0.43 ( 14807 hom., cov: 32)
Exomes 𝑓: 0.38 ( 26 hom. )

Consequence

ALOX12P1
ENST00000579299.2 upstream_gene

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0760

Publications

1 publications found
Variant links:
Genes affected
ALOX12P1 (HGNC:431): (arachidonate 12-lipoxygenase pseudogene 1)

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.93).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.816 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ALOX12P1ENST00000579299.2 linkn.-31T>G upstream_gene_variant 6

Frequencies

GnomAD3 genomes
AF:
0.430
AC:
65226
AN:
151860
Hom.:
14801
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.338
Gnomad AMI
AF:
0.466
Gnomad AMR
AF:
0.484
Gnomad ASJ
AF:
0.472
Gnomad EAS
AF:
0.836
Gnomad SAS
AF:
0.478
Gnomad FIN
AF:
0.410
Gnomad MID
AF:
0.417
Gnomad NFE
AF:
0.438
Gnomad OTH
AF:
0.450
GnomAD4 exome
AF:
0.375
AC:
165
AN:
440
Hom.:
26
Cov.:
0
AF XY:
0.354
AC XY:
95
AN XY:
268
show subpopulations
African (AFR)
AC:
0
AN:
0
American (AMR)
AC:
0
AN:
0
Ashkenazi Jewish (ASJ)
AC:
0
AN:
0
East Asian (EAS)
AC:
0
AN:
0
South Asian (SAS)
AC:
0
AN:
0
European-Finnish (FIN)
AF:
0.383
AC:
163
AN:
426
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
2
European-Non Finnish (NFE)
AF:
0.125
AC:
1
AN:
8
Other (OTH)
AF:
0.250
AC:
1
AN:
4
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.492
Heterozygous variant carriers
0
6
12
18
24
30
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome
AF:
0.429
AC:
65247
AN:
151980
Hom.:
14807
Cov.:
32
AF XY:
0.434
AC XY:
32257
AN XY:
74296
show subpopulations
African (AFR)
AF:
0.337
AC:
13988
AN:
41464
American (AMR)
AF:
0.484
AC:
7385
AN:
15256
Ashkenazi Jewish (ASJ)
AF:
0.472
AC:
1639
AN:
3470
East Asian (EAS)
AF:
0.837
AC:
4315
AN:
5158
South Asian (SAS)
AF:
0.478
AC:
2296
AN:
4802
European-Finnish (FIN)
AF:
0.410
AC:
4333
AN:
10564
Middle Eastern (MID)
AF:
0.422
AC:
124
AN:
294
European-Non Finnish (NFE)
AF:
0.438
AC:
29793
AN:
67960
Other (OTH)
AF:
0.452
AC:
950
AN:
2102
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
1829
3658
5487
7316
9145
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
610
1220
1830
2440
3050
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
0.425
Hom.:
2300
Bravo
AF:
0.434
Asia WGS
AF:
0.600
AC:
2087
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.93
CADD
Benign
9.8
DANN
Benign
0.75
PhyloP100
-0.076

Splicing

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

Publications

Other links and lift over

dbSNP: rs216465; hg19: chr17-28856675; API