chr10-49610828-C-A
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BA1
The NM_003055.3(SLC18A3):c.88C>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 0.00384 in 1,607,874 control chromosomes in the GnomAD database, including 211 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Synonymous variant affecting the same amino acid position (i.e. R30R) has been classified as Likely benign.
Frequency
Consequence
NM_003055.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -19 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC18A3 | NM_003055.3 | c.88C>A | p.Arg30= | synonymous_variant | 1/1 | ENST00000374115.5 | |
CHAT | NM_020984.4 | c.-69+1629C>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC18A3 | ENST00000374115.5 | c.88C>A | p.Arg30= | synonymous_variant | 1/1 | NM_003055.3 | P1 | ||
CHAT | ENST00000339797.5 | c.-69+1629C>A | intron_variant | 1 | A2 |
Frequencies
GnomAD3 genomes AF: 0.0209 AC: 3183AN: 152248Hom.: 114 Cov.: 34
GnomAD3 exomes AF: 0.00534 AC: 1261AN: 236136Hom.: 45 AF XY: 0.00391 AC XY: 502AN XY: 128528
GnomAD4 exome AF: 0.00205 AC: 2982AN: 1455508Hom.: 97 Cov.: 80 AF XY: 0.00176 AC XY: 1277AN XY: 723616
GnomAD4 genome AF: 0.0209 AC: 3188AN: 152366Hom.: 114 Cov.: 34 AF XY: 0.0202 AC XY: 1504AN XY: 74514
ClinVar
Submissions by phenotype
CHAT-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jul 19, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at