rs797045676
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 8P and 2B. PVS1_ModeratePM2PP3_StrongBP6_Moderate
The NM_001278116.2(L1CAM):c.91+1G>T variant causes a splice donor change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000912 in 1,096,723 control chromosomes in the GnomAD database, with no homozygous occurrence. There are no hemizygote samples in GnomAD. In-silico tool predicts a pathogenic outcome for this variant. 3/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_001278116.2 splice_donor
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
L1CAM | NM_001278116.2 | c.91+1G>T | splice_donor_variant | ENST00000370060.7 | |||
L1CAM | NM_000425.5 | c.91+1G>T | splice_donor_variant | ||||
L1CAM | NM_024003.3 | c.91+1G>T | splice_donor_variant | ||||
L1CAM | NM_001143963.2 | c.77-530G>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
L1CAM | ENST00000370060.7 | c.91+1G>T | splice_donor_variant | 5 | NM_001278116.2 | A1 |
Frequencies
GnomAD3 genomes ? Cov.: 24
GnomAD3 exomes AF: 0.00000545 AC: 1AN: 183473Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 67909
GnomAD4 exome AF: 9.12e-7 AC: 1AN: 1096723Hom.: 0 Cov.: 29 AF XY: 0.00 AC XY: 0AN XY: 362185
GnomAD4 genome ? Cov.: 24
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | May 21, 2015 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at