chr3-124735327-A-G
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_000373.4(UMPS):c.310+81A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.255 in 1,298,672 control chromosomes in the GnomAD database, including 45,051 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.23 ( 4455 hom., cov: 33)
Exomes 𝑓: 0.26 ( 40596 hom. )
Consequence
UMPS
NM_000373.4 intron
NM_000373.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.586
Genes affected
UMPS (HGNC:12563): (uridine monophosphate synthetase) This gene encodes a uridine 5'-monophosphate synthase. The encoded protein is a bifunctional enzyme that catalyzes the final two steps of the de novo pyrimidine biosynthetic pathway. The first reaction is carried out by the N-terminal enzyme orotate phosphoribosyltransferase which converts orotic acid to orotidine-5'-monophosphate. The terminal reaction is carried out by the C-terminal enzyme OMP decarboxylase which converts orotidine-5'-monophosphate to uridine monophosphate. Defects in this gene are the cause of hereditary orotic aciduria. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Mar 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.8).
BP6
Variant 3-124735327-A-G is Benign according to our data. Variant chr3-124735327-A-G is described in ClinVar as [Benign]. Clinvar id is 1249492.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.333 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
UMPS | NM_000373.4 | c.310+81A>G | intron_variant | ENST00000232607.7 | |||
UMPS | NR_033434.2 | n.177-2241A>G | intron_variant, non_coding_transcript_variant | ||||
UMPS | NR_033437.2 | n.429+81A>G | intron_variant, non_coding_transcript_variant | ||||
UMPS | XR_001740253.3 | n.330+81A>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
UMPS | ENST00000232607.7 | c.310+81A>G | intron_variant | 1 | NM_000373.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.227 AC: 34483AN: 152030Hom.: 4460 Cov.: 33
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GnomAD4 exome AF: 0.259 AC: 296951AN: 1146524Hom.: 40596 AF XY: 0.258 AC XY: 148684AN XY: 577300
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GnomAD4 genome AF: 0.227 AC: 34473AN: 152148Hom.: 4455 Cov.: 33 AF XY: 0.226 AC XY: 16808AN XY: 74366
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 19, 2021 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at