chr16-88809651-A-G
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_000485.3(APRT):c.*47T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0131 in 1,612,214 control chromosomes in the GnomAD database, including 306 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.019 ( 45 hom., cov: 34)
Exomes 𝑓: 0.013 ( 261 hom. )
Consequence
APRT
NM_000485.3 3_prime_UTR
NM_000485.3 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -2.53
Genes affected
APRT (HGNC:626): (adenine phosphoribosyltransferase) Adenine phosphoribosyltransferase belongs to the purine/pyrimidine phosphoribosyltransferase family. A conserved feature of this gene is the distribution of CpG dinucleotides. This enzyme catalyzes the formation of AMP and inorganic pyrophosphate from adenine and 5-phosphoribosyl-1-pyrophosphate (PRPP). It also produces adenine as a by-product of the polyamine biosynthesis pathway. A homozygous deficiency in this enzyme causes 2,8-dihydroxyadenine urolithiasis. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BP6
?
Variant 16-88809651-A-G is Benign according to our data. Variant chr16-88809651-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 321161.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0191 (2910/152262) while in subpopulation AFR AF= 0.0422 (1752/41538). AF 95% confidence interval is 0.0405. There are 45 homozygotes in gnomad4. There are 1392 alleles in male gnomad4 subpopulation. Median coverage is 34. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 44 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
APRT | NM_000485.3 | c.*47T>C | 3_prime_UTR_variant | 5/5 | ENST00000378364.8 | ||
APRT | NM_001030018.2 | c.*51T>C | 3_prime_UTR_variant | 5/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
APRT | ENST00000378364.8 | c.*47T>C | 3_prime_UTR_variant | 5/5 | 1 | NM_000485.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0190 AC: 2898AN: 152144Hom.: 44 Cov.: 34
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GnomAD3 exomes AF: 0.0149 AC: 3728AN: 249990Hom.: 67 AF XY: 0.0165 AC XY: 2231AN XY: 135502
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GnomAD4 exome AF: 0.0125 AC: 18255AN: 1459952Hom.: 261 Cov.: 31 AF XY: 0.0135 AC XY: 9821AN XY: 726268
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GnomAD4 genome ? AF: 0.0191 AC: 2910AN: 152262Hom.: 45 Cov.: 34 AF XY: 0.0187 AC XY: 1392AN XY: 74472
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ClinVar
Significance: Likely benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Adenine phosphoribosyltransferase deficiency Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Morquio syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Oct 19, 2018 | - - |
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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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at