dbSNP rs4732038: AKR1B15:c.150+801A>C (chr7-134565570-A-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_001080538.3(AKR1B15):c.150+801A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.513 in 1,612,442 control chromosomes in the GnomAD database, including 213,468 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 0.52 ( 20565 hom., cov: 32)

Exomes 𝑓: 0.51 ( 192903 hom. )

Consequence

AKR1B15
NM_001080538.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.917

Publications

18 publications found

Variant links:

Genes affected

AKR1B15 (HGNC:37281): (aldo-keto reductase family 1 member B15) Enables estradiol 17-beta-dehydrogenase activity. Predicted to be involved in estrogen biosynthetic process. Located in cytosol and mitochondrion. [provided by Alliance of Genome Resources, Apr 2022]

AKR1B15 links:

ENSG00000298133 (HGNC:):

ENSG00000298133 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=-0.93).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.564 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
AKR1B15	NM_001080538.3 link	c.150+801A>C		intron_variant	Intron 3 of 11	ENST00000457545.7	NP_001074007.2	C9JRZ8-2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
AKR1B15	ENST00000457545.7 link	c.150+801A>C		intron_variant	Intron 3 of 11	5	NM_001080538.3	ENSP00000389289.1		C9JRZ8-2

Frequencies

GnomAD3 genomes

AF:

0.519

AC:

78732

AN:

151816

Hom.:

20554

Cov.:

show subpopulations

Gnomad AFR

AF:

0.571

Gnomad AMI

AF:

0.438

Gnomad AMR

AF:

0.486

Gnomad ASJ

AF:

0.481

Gnomad EAS

AF:

0.458

Gnomad SAS

AF:

0.468

Gnomad FIN

AF:

0.463

Gnomad MID

AF:

0.415

Gnomad NFE

AF:

0.515

Gnomad OTH

AF:

0.502

GnomAD2 exomes

AF:

0.505

AC:

126101

AN:

249652

AF XY:

0.502

show subpopulations

Gnomad AFR exome

AF:

0.574

Gnomad AMR exome

AF:

0.508

Gnomad ASJ exome

AF:

0.482

Gnomad EAS exome

AF:

0.466

Gnomad FIN exome

AF:

0.468

Gnomad NFE exome

AF:

0.518

Gnomad OTH exome

AF:

0.486

GnomAD4 exome

AF:

0.513

AC:

748527

AN:

1460508

Hom.:

192903

Cov.:

AF XY:

0.511

AC XY:

371123

AN XY:

726512

show subpopulations

African (AFR)

AF:

0.575

AC:

19245

AN:

33448

American (AMR)

AF:

0.503

AC:

22415

AN:

44606

Ashkenazi Jewish (ASJ)

AF:

0.480

AC:

12535

AN:

26108

East Asian (EAS)

AF:

0.444

AC:

17566

AN:

39574

South Asian (SAS)

AF:

0.484

AC:

41744

AN:

86200

European-Finnish (FIN)

AF:

0.470

AC:

25068

AN:

53312

Middle Eastern (MID)

AF:

0.441

AC:

2535

AN:

5754

European-Non Finnish (NFE)

AF:

0.519

AC:

576680

AN:

1111170

Other (OTH)

AF:

0.509

AC:

30739

AN:

60336

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.488

Heterozygous variant carriers

19949

39898

59848

79797

99746

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

16640

33280

49920

66560

83200

<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:

0.519

AC:

78781

AN:

151934

Hom.:

20565

Cov.:

AF XY:

0.514

AC XY:

38127

AN XY:

74238

show subpopulations

African (AFR)

AF:

0.570

AC:

23610

AN:

41416

American (AMR)

AF:

0.486

AC:

7423

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.481

AC:

1668

AN:

3468

East Asian (EAS)

AF:

0.458

AC:

2362

AN:

5154

South Asian (SAS)

AF:

0.469

AC:

2262

AN:

4822

European-Finnish (FIN)

AF:

0.463

AC:

4876

AN:

10532

Middle Eastern (MID)

AF:

0.412

AC:

121

AN:

294

European-Non Finnish (NFE)

AF:

0.515

AC:

34998

AN:

67944

Other (OTH)

AF:

0.503

AC:

1062

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1983

3966

5950

7933

9916

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

700

1400

2100

2800

3500

<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:

0.511

Hom.:

15219

Bravo

AF:

0.523

Asia WGS

AF:

0.477

AC:

1657

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

2.4

(source)

DANN

Benign

0.45

PhyloP100

-0.92

PromoterAI

-0.072

Neutral

(source)

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