rs1057517666
Variant summary
Our verdict is Likely pathogenic. Variant got 8 ACMG points: 8P and 0B. PM2PM5PP3_Strong
The NM_003055.3(SLC18A3):c.1192G>A(p.Asp398Asn) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. D398H) has been classified as Likely pathogenic.
Frequency
Consequence
NM_003055.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC18A3 | NM_003055.3 | c.1192G>A | p.Asp398Asn | missense_variant | 1/1 | ENST00000374115.5 | |
CHAT | NM_020984.4 | c.-69+2733G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC18A3 | ENST00000374115.5 | c.1192G>A | p.Asp398Asn | missense_variant | 1/1 | NM_003055.3 | P1 | ||
CHAT | ENST00000339797.5 | c.-69+2733G>A | intron_variant | 1 | A2 |
Frequencies
GnomAD3 genomes AF: 0.00 AC: 0AN: 152210Hom.: 0 Cov.: 34 FAILED QC
GnomAD4 exome Cov.: 80
GnomAD4 genome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 152210Hom.: 0 Cov.: 34 AF XY: 0.00 AC XY: 0AN XY: 74356
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at