chrX-107628652-C-T
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Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4BP6_ModerateBP7BS2
The NM_002764.4(PRPS1):c.24C>T(p.Ser8=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000744 in 1,209,764 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 5 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0000090 ( 0 hom., 0 hem., cov: 23)
Exomes 𝑓: 0.0000073 ( 0 hom. 5 hem. )
Consequence
PRPS1
NM_002764.4 synonymous
NM_002764.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 2.75
Genes affected
PRPS1 (HGNC:9462): (phosphoribosyl pyrophosphate synthetase 1) This gene encodes an enzyme that catalyzes the phosphoribosylation of ribose 5-phosphate to 5-phosphoribosyl-1-pyrophosphate, which is necessary for purine metabolism and nucleotide biosynthesis. Defects in this gene are a cause of phosphoribosylpyrophosphate synthetase superactivity, Charcot-Marie-Tooth disease X-linked recessive type 5 and Arts Syndrome. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Feb 2011]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -8 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.14).
BP6
Variant X-107628652-C-T is Benign according to our data. Variant chrX-107628652-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 1157448.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=2.75 with no splicing effect.
BS2
High Hemizygotes in GnomAdExome4 at 5 XL gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PRPS1 | NM_002764.4 | c.24C>T | p.Ser8= | synonymous_variant | 1/7 | ENST00000372435.10 | |
PRPS1 | NM_001204402.2 | c.-181C>T | 5_prime_UTR_variant | 1/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PRPS1 | ENST00000372435.10 | c.24C>T | p.Ser8= | synonymous_variant | 1/7 | 1 | NM_002764.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00000897 AC: 1AN: 111524Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 33684
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GnomAD3 exomes AF: 0.0000163 AC: 3AN: 183488Hom.: 0 AF XY: 0.0000147 AC XY: 1AN XY: 67922
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GnomAD4 exome AF: 0.00000728 AC: 8AN: 1098188Hom.: 0 Cov.: 31 AF XY: 0.0000138 AC XY: 5AN XY: 363546
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GnomAD4 genome AF: 0.00000896 AC: 1AN: 111576Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 33746
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Charcot-Marie-Tooth Neuropathy X Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 09, 2023 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at