chr15-42945478-G-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_174916.3(UBR1):c.5109-8C>A 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 0.0000576 in 1,613,444 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_174916.3 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 |
---|---|---|---|---|---|---|---|
UBR1 | NM_174916.3 | c.5109-8C>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000290650.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
UBR1 | ENST00000290650.9 | c.5109-8C>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_174916.3 | P1 | |||
UBR1 | ENST00000562173.1 | n.314-8C>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000659 AC: 10AN: 151856Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000718 AC: 18AN: 250526Hom.: 0 AF XY: 0.0000664 AC XY: 9AN XY: 135484
GnomAD4 exome AF: 0.0000568 AC: 83AN: 1461588Hom.: 0 Cov.: 31 AF XY: 0.0000550 AC XY: 40AN XY: 727092
GnomAD4 genome AF: 0.0000659 AC: 10AN: 151856Hom.: 0 Cov.: 32 AF XY: 0.0000539 AC XY: 4AN XY: 74148
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 06, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at