chr5-1239471-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_182632.3(SLC6A18):c.754C>T(p.Arg252Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000107 in 1,613,900 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic 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. R252Q) has been classified as Likely benign.
Frequency
Consequence
NM_182632.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC6A18 | NM_182632.3 | c.754C>T | p.Arg252Trp | missense_variant | 6/12 | ENST00000324642.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC6A18 | ENST00000324642.4 | c.754C>T | p.Arg252Trp | missense_variant | 6/12 | 1 | NM_182632.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000985 AC: 15AN: 152244Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000557 AC: 14AN: 251376Hom.: 0 AF XY: 0.0000515 AC XY: 7AN XY: 135852
GnomAD4 exome AF: 0.000107 AC: 157AN: 1461656Hom.: 0 Cov.: 30 AF XY: 0.000100 AC XY: 73AN XY: 727150
GnomAD4 genome ? AF: 0.0000985 AC: 15AN: 152244Hom.: 0 Cov.: 33 AF XY: 0.0000807 AC XY: 6AN XY: 74378
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 11, 2021 | The c.754C>T (p.R252W) alteration is located in exon 6 (coding exon 6) of the SLC6A18 gene. This alteration results from a C to T substitution at nucleotide position 754, causing the arginine (R) at amino acid position 252 to be replaced by a tryptophan (W). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at