3-126488284-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_144639.3(UROC1):c.1709-5C>T 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 0.0000304 in 1,614,102 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 Uncertain significance (★).
Frequency
Consequence
NM_144639.3 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
UROC1 | NM_144639.3 | c.1709-5C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000290868.7 | |||
UROC1 | NM_001165974.2 | c.1889-5C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
UROC1 | ENST00000290868.7 | c.1709-5C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_144639.3 | P1 | |||
UROC1 | ENST00000383579.3 | c.1889-5C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000591 AC: 9AN: 152246Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.0000318 AC: 8AN: 251372Hom.: 0 AF XY: 0.0000294 AC XY: 4AN XY: 135866
GnomAD4 exome AF: 0.0000274 AC: 40AN: 1461856Hom.: 0 Cov.: 32 AF XY: 0.0000303 AC XY: 22AN XY: 727226
GnomAD4 genome ? AF: 0.0000591 AC: 9AN: 152246Hom.: 0 Cov.: 34 AF XY: 0.0000672 AC XY: 5AN XY: 74392
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genomic Diagnostic Laboratory, Division of Genomic Diagnostics, Children's Hospital of Philadelphia | Mar 06, 2015 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at