12-106427197-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM1PP2PP3
The NM_018082.6(POLR3B):c.1102C>T(p.Leu368Phe) variant causes a missense, splice region change involving the alteration of a conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 2/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. L368V) has been classified as Uncertain significance.
Frequency
Consequence
NM_018082.6 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
POLR3B | NM_018082.6 | c.1102C>T | p.Leu368Phe | missense_variant, splice_region_variant | 13/28 | ENST00000228347.9 | |
POLR3B | NM_001160708.2 | c.928C>T | p.Leu310Phe | missense_variant, splice_region_variant | 13/28 | ||
POLR3B | XM_017019621.3 | c.1102C>T | p.Leu368Phe | missense_variant, splice_region_variant | 13/26 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
POLR3B | ENST00000228347.9 | c.1102C>T | p.Leu368Phe | missense_variant, splice_region_variant | 13/28 | 1 | NM_018082.6 | P1 | |
POLR3B | ENST00000539066.5 | c.928C>T | p.Leu310Phe | missense_variant, splice_region_variant | 13/28 | 2 | |||
POLR3B | ENST00000549569.1 | c.376C>T | p.Leu126Phe | missense_variant, splice_region_variant | 5/5 | 4 | |||
POLR3B | ENST00000549195.1 | n.512C>T | splice_region_variant, non_coding_transcript_exon_variant | 3/3 | 3 |
Frequencies
GnomAD3 genomes AF: 0.00 AC: 100AN: 110352Hom.: 0 Cov.: 28 FAILED QC
GnomAD3 exomes AF: 0.0573 AC: 5962AN: 103986Hom.: 0 AF XY: 0.0606 AC XY: 3357AN XY: 55438
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00573 AC: 6592AN: 1149806Hom.: 0 Cov.: 24 AF XY: 0.00671 AC XY: 3829AN XY: 571052
GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.000906 AC: 100AN: 110402Hom.: 0 Cov.: 28 AF XY: 0.00103 AC XY: 54AN XY: 52470
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Jul 15, 2014 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at