chr10-5099338-G-A
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1
The NM_003739.6(AKR1C3):c.459G>A(p.Lys153=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0032 in 1,614,118 control chromosomes in the GnomAD database, including 138 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.017 ( 68 hom., cov: 32)
Exomes 𝑓: 0.0018 ( 70 hom. )
Consequence
AKR1C3
NM_003739.6 synonymous
NM_003739.6 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.00800
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 -15 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.63).
BP6
?
Variant 10-5099338-G-A is Benign according to our data. Variant chr10-5099338-G-A is described in ClinVar as [Benign]. Clinvar id is 779103.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=0.008 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0559 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AKR1C3 | NM_003739.6 | c.459G>A | p.Lys153= | synonymous_variant | 5/9 | ENST00000380554.5 | |
AKR1C3 | NM_001253908.2 | c.459G>A | p.Lys153= | synonymous_variant | 5/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AKR1C3 | ENST00000380554.5 | c.459G>A | p.Lys153= | synonymous_variant | 5/9 | 1 | NM_003739.6 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.0167 AC: 2543AN: 152124Hom.: 68 Cov.: 32
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GnomAD3 exomes AF: 0.00445 AC: 1119AN: 251428Hom.: 25 AF XY: 0.00347 AC XY: 471AN XY: 135890
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GnomAD4 exome AF: 0.00179 AC: 2617AN: 1461876Hom.: 70 Cov.: 31 AF XY: 0.00156 AC XY: 1131AN XY: 727234
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GnomAD4 genome ? AF: 0.0167 AC: 2548AN: 152242Hom.: 68 Cov.: 32 AF XY: 0.0157 AC XY: 1172AN XY: 74418
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
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Dann
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at