10-117241742-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_003054.6(SLC18A2):c.49C>T(p.Arg17Cys) variant causes a missense change. The variant allele was found at a frequency of 0.000492 in 1,609,854 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 Uncertain significance (★★). Synonymous variant affecting the same amino acid position (i.e. R17R) has been classified as Likely benign.
Frequency
Consequence
NM_003054.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC18A2 | NM_003054.6 | c.49C>T | p.Arg17Cys | missense_variant | 2/16 | ENST00000644641.2 | |
SLC18A2-AS1 | NR_184309.1 | n.113+143G>A | intron_variant, non_coding_transcript_variant | ||||
SLC18A2-AS1 | NR_184310.1 | n.155G>A | non_coding_transcript_exon_variant | 2/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC18A2 | ENST00000644641.2 | c.49C>T | p.Arg17Cys | missense_variant | 2/16 | NM_003054.6 | P1 | ||
SLC18A2-AS1 | ENST00000425264.2 | n.156G>A | non_coding_transcript_exon_variant | 2/3 | 3 | ||||
SLC18A2 | ENST00000497497.1 | n.192C>T | non_coding_transcript_exon_variant | 2/15 | 2 | ||||
SLC18A2-AS1 | ENST00000691914.2 | n.113+143G>A | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.000296 AC: 45AN: 152214Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000266 AC: 63AN: 237006Hom.: 0 AF XY: 0.000224 AC XY: 29AN XY: 129536
GnomAD4 exome AF: 0.000512 AC: 747AN: 1457640Hom.: 0 Cov.: 33 AF XY: 0.000452 AC XY: 328AN XY: 724980
GnomAD4 genome ? AF: 0.000296 AC: 45AN: 152214Hom.: 0 Cov.: 33 AF XY: 0.000242 AC XY: 18AN XY: 74356
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 26, 2023 | The c.49C>T (p.R17C) alteration is located in exon 2 (coding exon 1) of the SLC18A2 gene. This alteration results from a C to T substitution at nucleotide position 49, causing the arginine (R) at amino acid position 17 to be replaced by a cysteine (C). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Aug 04, 2022 | This sequence change replaces arginine, which is basic and polar, with cysteine, which is neutral and slightly polar, at codon 17 of the SLC18A2 protein (p.Arg17Cys). This variant is present in population databases (rs148348449, gnomAD 0.05%). This variant has not been reported in the literature in individuals affected with SLC18A2-related conditions. Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at