10-49610830-G-A
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_003055.3(SLC18A3):c.90G>A(p.Arg30=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000211 in 1,608,424 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. R30R) has been classified as Benign.
Frequency
Consequence
NM_003055.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC18A3 | NM_003055.3 | c.90G>A | p.Arg30= | synonymous_variant | 1/1 | ENST00000374115.5 | |
CHAT | NM_020984.4 | c.-69+1631G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC18A3 | ENST00000374115.5 | c.90G>A | p.Arg30= | synonymous_variant | 1/1 | NM_003055.3 | P1 | ||
CHAT | ENST00000339797.5 | c.-69+1631G>A | intron_variant | 1 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152270Hom.: 0 Cov.: 34
GnomAD4 exome AF: 0.0000227 AC: 33AN: 1456154Hom.: 0 Cov.: 80 AF XY: 0.0000193 AC XY: 14AN XY: 724018
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152270Hom.: 0 Cov.: 34 AF XY: 0.00 AC XY: 0AN XY: 74394
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Sep 01, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at