15-74823554-G-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_021819.3(LMAN1L):c.1200-5G>T variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_021819.3 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 |
---|---|---|---|---|---|---|---|
LMAN1L | NM_021819.3 | c.1200-5G>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000309664.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LMAN1L | ENST00000309664.10 | c.1200-5G>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_021819.3 | P1 | |||
LMAN1L | ENST00000379709.7 | c.1164-5G>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | |||||
LMAN1L | ENST00000567848.1 | c.242+845G>T | intron_variant | 4 | |||||
LMAN1L | ENST00000565585.5 | n.1594-5G>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 31
GnomAD4 exome Cov.: 42
GnomAD4 genome ? Cov.: 31
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at