rs11474
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The ENST00000380753.9(AKR1C2):c.515T>A(p.Leu172Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00028 in 1,614,116 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
ENST00000380753.9 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
AKR1C2 | NM_001393392.1 | c.515T>A | p.Leu172Gln | missense_variant | 5/9 | ENST00000380753.9 | NP_001380321.1 | |
LOC101928051 | XR_001747340.2 | n.1779A>T | non_coding_transcript_exon_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
AKR1C2 | ENST00000380753.9 | c.515T>A | p.Leu172Gln | missense_variant | 5/9 | 1 | NM_001393392.1 | ENSP00000370129 | P1 | |
AKR1C2 | ENST00000421196.7 | c.437T>A | p.Leu146Gln | missense_variant | 4/8 | 1 | ENSP00000392694 | |||
AKR1C2 | ENST00000604507.5 | c.515T>A | p.Leu172Gln | missense_variant | 6/7 | 5 | ENSP00000474566 | |||
AKR1C2 | ENST00000460124.5 | n.1975T>A | non_coding_transcript_exon_variant | 4/8 | 5 |
Frequencies
GnomAD3 genomes AF: 0.000256 AC: 39AN: 152182Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000119 AC: 30AN: 251446Hom.: 0 AF XY: 0.000140 AC XY: 19AN XY: 135896
GnomAD4 exome AF: 0.000283 AC: 413AN: 1461814Hom.: 0 Cov.: 31 AF XY: 0.000286 AC XY: 208AN XY: 727212
GnomAD4 genome AF: 0.000256 AC: 39AN: 152302Hom.: 0 Cov.: 32 AF XY: 0.000188 AC XY: 14AN XY: 74462
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at