chr3-197675519-G-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_014687.4(RUBCN):c.2647-4C>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 0.00000496 in 1,612,344 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_014687.4 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RUBCN | NM_014687.4 | c.2647-4C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000296343.10 | NP_055502.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RUBCN | ENST00000296343.10 | c.2647-4C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_014687.4 | ENSP00000296343 | P1 | |||
RUBCN | ENST00000273582.9 | c.2512-4C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 5 | ENSP00000273582 | |||||
RUBCN | ENST00000413360.5 | c.2531-4C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 5 | ENSP00000405115 | |||||
RUBCN | ENST00000707076.1 | c.2764-4C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENSP00000516727 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152188Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000402 AC: 1AN: 249012Hom.: 0 AF XY: 0.00000740 AC XY: 1AN XY: 135138
GnomAD4 exome AF: 0.00000342 AC: 5AN: 1460156Hom.: 0 Cov.: 31 AF XY: 0.00000413 AC XY: 3AN XY: 726474
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152188Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74348
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Oct 17, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at