rs4732038
Positions:
Variant summary
Our verdict is Benign. Variant got -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
NM_001080538.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.917
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]
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=-0.93).
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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AKR1B15 | NM_001080538.3 | c.150+801A>C | intron_variant | ENST00000457545.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AKR1B15 | ENST00000457545.7 | c.150+801A>C | intron_variant | 5 | NM_001080538.3 | ||||
AKR1B15 | ENST00000467156.1 | n.759+24A>C | intron_variant, non_coding_transcript_variant | 1 | |||||
AKR1B15 | ENST00000423958.2 | c.150+801A>C | intron_variant | 5 | |||||
AKR1B15 | ENST00000652743.1 | c.66+24A>C | intron_variant | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.519 AC: 78732AN: 151816Hom.: 20554 Cov.: 32
GnomAD3 genomes
?
AF:
AC:
78732
AN:
151816
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.505 AC: 126101AN: 249652Hom.: 31937 AF XY: 0.502 AC XY: 67797AN XY: 134930
GnomAD3 exomes
AF:
AC:
126101
AN:
249652
Hom.:
AF XY:
AC XY:
67797
AN XY:
134930
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.513 AC: 748527AN: 1460508Hom.: 192903 Cov.: 53 AF XY: 0.511 AC XY: 371123AN XY: 726512
GnomAD4 exome
AF:
AC:
748527
AN:
1460508
Hom.:
Cov.:
53
AF XY:
AC XY:
371123
AN XY:
726512
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? AF: 0.519 AC: 78781AN: 151934Hom.: 20565 Cov.: 32 AF XY: 0.514 AC XY: 38127AN XY: 74238
GnomAD4 genome
?
AF:
AC:
78781
AN:
151934
Hom.:
Cov.:
32
AF XY:
AC XY:
38127
AN XY:
74238
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
1657
AN:
3476
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at