chr10-5102114-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_ModerateBP6_Moderate
The NM_003739.6(AKR1C3):c.584C>T(p.Pro195Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000386 in 1,611,672 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_003739.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AKR1C3 | NM_003739.6 | c.584C>T | p.Pro195Leu | missense_variant | 6/9 | ENST00000380554.5 | |
AKR1C3 | NM_001253908.2 | c.584C>T | p.Pro195Leu | missense_variant | 6/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AKR1C3 | ENST00000380554.5 | c.584C>T | p.Pro195Leu | missense_variant | 6/9 | 1 | NM_003739.6 | P4 | |
AKR1C3 | ENST00000439082.7 | c.584C>T | p.Pro195Leu | missense_variant | 6/9 | 5 | A1 | ||
AKR1C3 | ENST00000605149.5 | c.515C>T | p.Pro172Leu | missense_variant | 6/9 | 2 | |||
AKR1C3 | ENST00000605781.5 | n.763C>T | non_coding_transcript_exon_variant | 6/6 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.000375 AC: 57AN: 152034Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000514 AC: 129AN: 251210Hom.: 1 AF XY: 0.000633 AC XY: 86AN XY: 135772
GnomAD4 exome AF: 0.000386 AC: 563AN: 1459520Hom.: 2 Cov.: 30 AF XY: 0.000410 AC XY: 298AN XY: 726252
GnomAD4 genome ? AF: 0.000388 AC: 59AN: 152152Hom.: 0 Cov.: 33 AF XY: 0.000349 AC XY: 26AN XY: 74392
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jul 21, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at