3-124735089-A-G
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_000373.4(UMPS):c.157-4A>G variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000342 in 1,460,454 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_000373.4 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
UMPS | NM_000373.4 | c.157-4A>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000232607.7 | |||
UMPS | NR_033434.2 | n.177-2479A>G | intron_variant, non_coding_transcript_variant | ||||
UMPS | NR_033437.2 | n.276-4A>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant | ||||
UMPS | XR_001740253.3 | n.177-4A>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
UMPS | ENST00000232607.7 | c.157-4A>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_000373.4 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD3 exomes AF: 0.00000796 AC: 2AN: 251182Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135770
GnomAD4 exome AF: 0.00000342 AC: 5AN: 1460454Hom.: 0 Cov.: 30 AF XY: 0.00000138 AC XY: 1AN XY: 726560
GnomAD4 genome ? Cov.: 33
ClinVar
Submissions by phenotype
Hereditary orotic aciduria, type 1 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jun 01, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at