rs3763676
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001253908.2(AKR1C3):c.85-2103A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.293 in 869,958 control chromosomes in the GnomAD database, including 44,687 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 0.34 ( 8386 hom., cov: 23)
Exomes 𝑓: 0.28 ( 36301 hom. )
Consequence
AKR1C3
NM_001253908.2 intron
NM_001253908.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.499
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=-0.89).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.363 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
AKR1C3 | NM_001253908.2 | c.85-2103A>G | intron_variant | NP_001240837.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
AKR1C3 | ENST00000439082.7 | c.85-2103A>G | intron_variant | 5 | ENSP00000401327 | A1 | ||||
AKR1C3 | ENST00000602997.5 | c.16-2103A>G | intron_variant | 3 | ENSP00000474188 | |||||
AKR1C3 | ENST00000605149.5 | c.16-2103A>G | intron_variant | 2 | ENSP00000474882 |
Frequencies
GnomAD3 genomes AF: 0.342 AC: 48330AN: 141336Hom.: 8378 Cov.: 23
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GnomAD4 exome AF: 0.284 AC: 206544AN: 728526Hom.: 36301 Cov.: 10 AF XY: 0.282 AC XY: 108503AN XY: 384344
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GnomAD4 genome AF: 0.342 AC: 48374AN: 141432Hom.: 8386 Cov.: 23 AF XY: 0.344 AC XY: 23422AN XY: 68030
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at