3-155893698-C-T
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 1P and 4B. PP3BS2
The NM_003875.3(GMPS):c.208C>T(p.Arg70Cys) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000128 in 1,568,152 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_003875.3 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GMPS | NM_003875.3 | c.208C>T | p.Arg70Cys | missense_variant, splice_region_variant | Exon 2 of 16 | ENST00000496455.7 | NP_003866.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GMPS | ENST00000496455.7 | c.208C>T | p.Arg70Cys | missense_variant, splice_region_variant | Exon 2 of 16 | 1 | NM_003875.3 | ENSP00000419851.1 | ||
GMPS | ENST00000295920.7 | c.28-10165C>T | intron_variant | Intron 1 of 13 | 2 | ENSP00000295920.7 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152080Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.0000106 AC: 15AN: 1415954Hom.: 0 Cov.: 24 AF XY: 0.00000708 AC XY: 5AN XY: 706064
GnomAD4 genome AF: 0.0000329 AC: 5AN: 152198Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74420
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.208C>T (p.R70C) alteration is located in exon 2 (coding exon 2) of the GMPS gene. This alteration results from a C to T substitution at nucleotide position 208, causing the arginine (R) at amino acid position 70 to be replaced by a cysteine (C). 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