15-58175002-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_020980.5(AQP9):c.461C>T(p.Pro154Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000669 in 1,614,114 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_020980.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
AQP9 | NM_020980.5 | c.461C>T | p.Pro154Leu | missense_variant | Exon 4 of 6 | ENST00000219919.9 | NP_066190.2 | |
AQP9 | NM_001320636.1 | c.266C>T | p.Pro89Leu | missense_variant | Exon 4 of 6 | NP_001307565.1 | ||
AQP9 | NM_001320635.2 | c.461C>T | p.Pro154Leu | missense_variant | Exon 4 of 5 | NP_001307564.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 152198Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000398 AC: 10AN: 251234Hom.: 0 AF XY: 0.0000295 AC XY: 4AN XY: 135776
GnomAD4 exome AF: 0.0000684 AC: 100AN: 1461798Hom.: 0 Cov.: 31 AF XY: 0.0000550 AC XY: 40AN XY: 727202
GnomAD4 genome AF: 0.0000525 AC: 8AN: 152316Hom.: 0 Cov.: 33 AF XY: 0.0000537 AC XY: 4AN XY: 74480
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.461C>T (p.P154L) alteration is located in exon 4 (coding exon 4) of the AQP9 gene. This alteration results from a C to T substitution at nucleotide position 461, causing the proline (P) at amino acid position 154 to be replaced by a leucine (L). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at