chrX-107628640-C-T
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_ModerateBP6_Very_StrongBP7BS2
The NM_002764.4(PRPS1):c.12C>T(p.Ile4Ile) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000364 in 1,098,180 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 (★★).
Frequency
Consequence
NM_002764.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -15 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00 AC: 1AN: 111702Hom.: 0 Cov.: 23 AF XY: 0.0000295 AC XY: 1AN XY: 33850 FAILED QC
GnomAD3 exomes AF: 0.0000109 AC: 2AN: 183496Hom.: 0 AF XY: 0.0000294 AC XY: 2AN XY: 67932
GnomAD4 exome AF: 0.00000364 AC: 4AN: 1098180Hom.: 0 Cov.: 31 AF XY: 0.00000825 AC XY: 3AN XY: 363544
GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000895 AC: 1AN: 111702Hom.: 0 Cov.: 23 AF XY: 0.0000295 AC XY: 1AN XY: 33850
ClinVar
Submissions by phenotype
not specified Benign:1
p.Ile4Ile in exon 1 of PRPS1: This variant is not expected to have clinical sign ificance because it does not alter an amino acid residue and is not located with in the splice consensus sequence. It has been identified in 2/47937 European chr omosomes by the Exome Aggregation Consortium (ExAC, http://exac.broadinstitute.o rg; dbSNP rs752590804). -
Charcot-Marie-Tooth Neuropathy X Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at