X-153648006-C-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_001318503.2(DUSP9):c.53C>A(p.Pro18Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000404 in 988,958 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 2 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P18L) has been classified as Uncertain significance.
Frequency
Consequence
NM_001318503.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DUSP9 | NM_001318503.2 | c.53C>A | p.Pro18Gln | missense_variant | 2/4 | ENST00000342782.4 | |
DUSP9 | NM_001395.4 | c.53C>A | p.Pro18Gln | missense_variant | 2/4 | ||
DUSP9 | XM_011531123.2 | c.146C>A | p.Pro49Gln | missense_variant | 2/4 | ||
DUSP9 | XM_047441899.1 | c.119C>A | p.Pro40Gln | missense_variant | 2/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DUSP9 | ENST00000342782.4 | c.53C>A | p.Pro18Gln | missense_variant | 2/4 | 1 | NM_001318503.2 | P1 | |
DUSP9 | ENST00000370167.8 | c.53C>A | p.Pro18Gln | missense_variant | 2/4 | 1 | P1 | ||
DUSP9 | ENST00000477033.1 | n.423C>A | non_coding_transcript_exon_variant | 3/3 | 3 |
Frequencies
GnomAD3 genomes Cov.: 24
GnomAD3 exomes AF: 0.0000681 AC: 3AN: 44044Hom.: 0 AF XY: 0.000101 AC XY: 1AN XY: 9862
GnomAD4 exome AF: 0.00000404 AC: 4AN: 988958Hom.: 0 Cov.: 30 AF XY: 0.00000635 AC XY: 2AN XY: 315208
GnomAD4 genome Cov.: 24
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at