dbSNP rs11568131: ALOX15:c.*287C>T (chr17-4631313-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_001140.5(ALOX15):c.*287C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.117 in 444,254 control chromosomes in the GnomAD database, including 3,805 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 0.11 ( 1165 hom., cov: 32)

Exomes 𝑓: 0.12 ( 2640 hom. )

Consequence

ALOX15
NM_001140.5 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.52

Publications

13 publications found

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]

ALOX15 Gene-Disease associations (from GenCC):

pregnancy loss, recurrent, susceptibility
Inheritance: AR Classification: LIMITED Submitted by: Ambry Genetics

ALOX15 links:

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=-0.97).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.156 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ALOX15	NM_001140.5 link	c.*287C>T		3_prime_UTR_variant	Exon 14 of 14	ENST00000293761.8	NP_001131.3	P16050-1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
ALOX15	ENST00000293761.8 link	c.*287C>T	3_prime_UTR_variant	Exon 14 of 14	1	NM_001140.5	ENSP00000293761.3	P16050-1
ALOX15	ENST00000570836.6 link	c.*287C>T	downstream_gene_variant		2		ENSP00000458832.1	P16050-1
ALOX15	ENST00000574640.1 link	c.*287C>T	downstream_gene_variant		2		ENSP00000460483.1	P16050-2

Frequencies

GnomAD3 genomes

AF:

0.110

AC:

16732

AN:

152162

Hom.:

1164

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0303

Gnomad AMI

AF:

0.194

Gnomad AMR

AF:

0.144

Gnomad ASJ

AF:

0.131

Gnomad EAS

AF:

0.00173

Gnomad SAS

AF:

0.0563

Gnomad FIN

AF:

0.123

Gnomad MID

AF:

0.171

Gnomad NFE

AF:

0.158

Gnomad OTH

AF:

0.129

GnomAD4 exome

AF:

0.120

AC:

35093

AN:

291974

Hom.:

2640

Cov.:

AF XY:

0.119

AC XY:

17926

AN XY:

150760

show subpopulations

African (AFR)

AF:

0.0250

AC:

243

AN:

9712

American (AMR)

AF:

0.126

AC:

1383

AN:

10976

Ashkenazi Jewish (ASJ)

AF:

0.126

AC:

1213

AN:

9600

East Asian (EAS)

AF:

0.000538

AC:

AN:

22302

South Asian (SAS)

AF:

0.0556

AC:

1167

AN:

20988

European-Finnish (FIN)

AF:

0.115

AC:

2184

AN:

19026

Middle Eastern (MID)

AF:

0.113

AC:

158

AN:

1398

European-Non Finnish (NFE)

AF:

0.147

AC:

26508

AN:

179894

Other (OTH)

AF:

0.123

AC:

2225

AN:

18078

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.492

Heterozygous variant carriers

1393

2787

4180

5574

6967

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

134

268

402

536

670

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.110

AC:

16736

AN:

152280

Hom.:

1165

Cov.:

AF XY:

0.108

AC XY:

8035

AN XY:

74450

show subpopulations

African (AFR)

AF:

0.0302

AC:

1256

AN:

41564

American (AMR)

AF:

0.144

AC:

2200

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.131

AC:

454

AN:

3468

East Asian (EAS)

AF:

0.00173

AC:

AN:

5192

South Asian (SAS)

AF:

0.0561

AC:

271

AN:

4830

European-Finnish (FIN)

AF:

0.123

AC:

1300

AN:

10598

Middle Eastern (MID)

AF:

0.170

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.158

AC:

10749

AN:

68016

Other (OTH)

AF:

0.128

AC:

270

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

767

1535

2302

3070

3837

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

176

352

528

704

880

<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:

0.127

Hom.:

1367

Bravo

AF:

0.108

Asia WGS

AF:

0.0280

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.97

CADD

Benign

0.11

(source)

DANN

Benign

0.28

PhyloP100

-3.5

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over