X-107642407-G-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4_ModerateBP6_ModerateBP7
The NM_002764.4(PRPS1):c.447G>T(p.Pro149=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000273 in 1,097,905 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 3 hemizygotes in GnomAD. 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. P149P) has been classified as Likely benign.
Frequency
Consequence
NM_002764.4 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 |
---|---|---|---|---|---|---|---|
PRPS1 | NM_002764.4 | c.447G>T | p.Pro149= | synonymous_variant | 4/7 | ENST00000372435.10 | |
PRPS1 | NM_001204402.2 | c.-82-2770G>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PRPS1 | ENST00000372435.10 | c.447G>T | p.Pro149= | synonymous_variant | 4/7 | 1 | NM_002764.4 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 23
GnomAD3 exomes AF: 0.00000545 AC: 1AN: 183471Hom.: 0 AF XY: 0.0000147 AC XY: 1AN XY: 67919
GnomAD4 exome AF: 0.00000273 AC: 3AN: 1097905Hom.: 0 Cov.: 30 AF XY: 0.00000826 AC XY: 3AN XY: 363275
GnomAD4 genome ? Cov.: 23
ClinVar
Submissions by phenotype
Charcot-Marie-Tooth Neuropathy X Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Feb 02, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at