chr1-19081341-G-A
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_020765.3(UBR4):c.15233+8C>T variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000689 in 1,582,086 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_020765.3 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
UBR4 | NM_020765.3 | c.15233+8C>T | splice_region_variant, intron_variant | ENST00000375254.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
UBR4 | ENST00000375254.8 | c.15233+8C>T | splice_region_variant, intron_variant | 1 | NM_020765.3 | P1 | |||
UBR4 | ENST00000375224.1 | c.2354+8C>T | splice_region_variant, intron_variant | 2 | |||||
UBR4 | ENST00000375225.7 | c.458+8C>T | splice_region_variant, intron_variant | 2 | |||||
UBR4 | ENST00000459947.5 | upstream_gene_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000526 AC: 8AN: 152144Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000397 AC: 9AN: 226654Hom.: 0 AF XY: 0.0000244 AC XY: 3AN XY: 123170
GnomAD4 exome AF: 0.0000706 AC: 101AN: 1429822Hom.: 0 Cov.: 30 AF XY: 0.0000677 AC XY: 48AN XY: 709450
GnomAD4 genome ? AF: 0.0000525 AC: 8AN: 152264Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74468
ClinVar
Submissions by phenotype
UBR4-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jun 10, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Apr 06, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at