15-58166710-G-T
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_020980.5(AQP9):c.149G>T(p.Ser50Ile) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000198 in 1,613,148 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 Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
AQP9 | NM_020980.5 | c.149G>T | p.Ser50Ile | missense_variant | Exon 2 of 6 | ENST00000219919.9 | NP_066190.2 | |
AQP9 | NM_001320635.2 | c.149G>T | p.Ser50Ile | missense_variant | Exon 2 of 5 | NP_001307564.1 | ||
AQP9 | NM_001320636.1 | c.-47G>T | 5_prime_UTR_variant | Exon 2 of 6 | NP_001307565.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000788 AC: 12AN: 152210Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000104 AC: 26AN: 250266Hom.: 0 AF XY: 0.0000887 AC XY: 12AN XY: 135264
GnomAD4 exome AF: 0.000210 AC: 307AN: 1460938Hom.: 0 Cov.: 30 AF XY: 0.000193 AC XY: 140AN XY: 726804
GnomAD4 genome AF: 0.0000788 AC: 12AN: 152210Hom.: 0 Cov.: 32 AF XY: 0.0000942 AC XY: 7AN XY: 74348
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.149G>T (p.S50I) alteration is located in exon 2 (coding exon 2) of the AQP9 gene. This alteration results from a G to T substitution at nucleotide position 149, causing the serine (S) at amino acid position 50 to be replaced by an isoleucine (I). 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