chr10-4967001-T-C
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Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP7BS2
The NM_001353.6(AKR1C1):āc.327T>Cā(p.Asp109=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00749 in 1,613,436 control chromosomes in the GnomAD database, including 45 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: š 0.0072 ( 4 hom., cov: 33)
Exomes š: 0.0075 ( 41 hom. )
Consequence
AKR1C1
NM_001353.6 synonymous
NM_001353.6 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.29
Genes affected
AKR1C1 (HGNC:384): (aldo-keto reductase family 1 member C1) 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 reaction of progesterone to the inactive form 20-alpha-hydroxy-progesterone. This gene shares high sequence identity with three other gene members and is clustered with those three genes at chromosome 10p15-p14. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -9 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.68).
BP7
Synonymous conserved (PhyloP=-1.29 with no splicing effect.
BS2
High Homozygotes in GnomAd4 at 4 AR gene
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| AKR1C1 | NM_001353.6 | c.327T>C | p.Asp109= | synonymous_variant | 3/9 | ENST00000380872.9 | NP_001344.2 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| AKR1C1 | ENST00000380872.9 | c.327T>C | p.Asp109= | synonymous_variant | 3/9 | 1 | NM_001353.6 | ENSP00000370254 | P1 |
Frequencies
GnomAD3 genomes 0.00714 AC: 1086AN: 152202Hom.: 4 Cov.: 33
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GnomAD3 exomes AF: 0.00601 AC: 1509AN: 251054Hom.: 8 AF XY: 0.00601 AC XY: 815AN XY: 135668
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GnomAD4 exome AF: 0.00752 AC: 10986AN: 1461116Hom.: 41 Cov.: 30 AF XY: 0.00736 AC XY: 5349AN XY: 726856
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GnomAD4 genome 0.00716 AC: 1091AN: 152320Hom.: 4 Cov.: 33 AF XY: 0.00698 AC XY: 520AN XY: 74502
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Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
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DANN
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RBP_binding_hub_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