chrX-134473344-AT-A
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Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_ModerateBS2
The NM_000194.3(HPRT1):c.28-14del variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000173 in 937,769 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 46 hemizygotes in GnomAD. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.00013 ( 0 hom., 5 hem., cov: 23)
Exomes 𝑓: 0.00018 ( 0 hom. 41 hem. )
Consequence
HPRT1
NM_000194.3 splice_polypyrimidine_tract, intron
NM_000194.3 splice_polypyrimidine_tract, intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.823
Genes affected
HPRT1 (HGNC:5157): (hypoxanthine phosphoribosyltransferase 1) The protein encoded by this gene is a transferase, which catalyzes conversion of hypoxanthine to inosine monophosphate and guanine to guanosine monophosphate via transfer of the 5-phosphoribosyl group from 5-phosphoribosyl 1-pyrophosphate. This enzyme plays a central role in the generation of purine nucleotides through the purine salvage pathway. Mutations in this gene result in Lesch-Nyhan syndrome or gout.[provided by RefSeq, Jun 2009]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -6 ACMG points.
BP6
Variant X-134473344-AT-A is Benign according to our data. Variant chrX-134473344-AT-A is described in ClinVar as [Benign]. Clinvar id is 2043338.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High Hemizygotes in GnomAd4 at 5 XL gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HPRT1 | NM_000194.3 | c.28-14del | splice_polypyrimidine_tract_variant, intron_variant | ENST00000298556.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HPRT1 | ENST00000298556.8 | c.28-14del | splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_000194.3 | P1 | |||
HPRT1 | ENST00000462974.5 | n.186-14del | splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant | 3 | |||||
HPRT1 | ENST00000475720.1 | upstream_gene_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.000134 AC: 15AN: 112104Hom.: 0 Cov.: 23 AF XY: 0.000146 AC XY: 5AN XY: 34266
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GnomAD3 exomes AF: 0.000115 AC: 21AN: 183048Hom.: 0 AF XY: 0.000177 AC XY: 12AN XY: 67606
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GnomAD4 exome AF: 0.000178 AC: 147AN: 825665Hom.: 0 Cov.: 15 AF XY: 0.000173 AC XY: 41AN XY: 236881
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GnomAD4 genome AF: 0.000134 AC: 15AN: 112104Hom.: 0 Cov.: 23 AF XY: 0.000146 AC XY: 5AN XY: 34266
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Lesch-Nyhan syndrome;C0268117:Partial hypoxanthine-guanine phosphoribosyltransferase deficiency Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Computational scores
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at