rs2275928
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_003739.6(AKR1C3):c.929+40G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.572 in 1,515,468 control chromosomes in the GnomAD database, including 255,408 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 0.58 ( 26266 hom., cov: 31)
Exomes 𝑓: 0.57 ( 229142 hom. )
Consequence
AKR1C3
NM_003739.6 intron
NM_003739.6 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.786
Genes affected
AKR1C3 (HGNC:386): (aldo-keto reductase family 1 member C3) This gene encodes a member of the aldo/keto reductase superfamily, which consists of more than 40 known enzymes and proteins. These enzymes catalyze the conversion of aldehydes and ketones to their corresponding alcohols by utilizing NADH and/or NADPH as cofactors. The enzymes display overlapping but distinct substrate specificity. This enzyme catalyzes the reduction of prostaglandin (PG) D2, PGH2 and phenanthrenequinone (PQ), and the oxidation of 9alpha,11beta-PGF2 to PGD2. It may play an important role in the pathogenesis of allergic diseases such as asthma, and may also have a role in controlling cell growth and/or differentiation. This gene shares high sequence identity with three other gene members and is clustered with those three genes at chromosome 10p15-p14. Three transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2011]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.633 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AKR1C3 | NM_003739.6 | c.929+40G>A | intron_variant | ENST00000380554.5 | |||
AKR1C3 | NM_001253908.2 | c.929+40G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AKR1C3 | ENST00000380554.5 | c.929+40G>A | intron_variant | 1 | NM_003739.6 | P4 | |||
AKR1C3 | ENST00000439082.7 | c.929+40G>A | intron_variant | 5 | A1 | ||||
AKR1C3 | ENST00000605149.5 | c.860+40G>A | intron_variant | 2 | |||||
AKR1C3 | ENST00000603484.1 | n.403+40G>A | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.580 AC: 88141AN: 151944Hom.: 26230 Cov.: 31
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GnomAD3 exomes AF: 0.519 AC: 117209AN: 225638Hom.: 32339 AF XY: 0.519 AC XY: 62958AN XY: 121316
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GnomAD4 exome AF: 0.571 AC: 778970AN: 1363406Hom.: 229142 Cov.: 19 AF XY: 0.567 AC XY: 386751AN XY: 681820
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GnomAD4 genome ? AF: 0.580 AC: 88229AN: 152062Hom.: 26266 Cov.: 31 AF XY: 0.575 AC XY: 42734AN XY: 74310
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at