rs781830365
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 2P and 3B. PM2BP4BP6_Moderate
The NM_001278116.2(L1CAM):c.1187C>A(p.Pro396His) variant causes a missense 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. Variant has been reported in ClinVar as Likely benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P396L) has been classified as Uncertain significance.
Frequency
Consequence
NM_001278116.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
L1CAM | NM_001278116.2 | c.1187C>A | p.Pro396His | missense_variant | 11/29 | ENST00000370060.7 | |
L1CAM | NM_000425.5 | c.1187C>A | p.Pro396His | missense_variant | 10/28 | ||
L1CAM | NM_024003.3 | c.1187C>A | p.Pro396His | missense_variant | 10/27 | ||
L1CAM | NM_001143963.2 | c.1172C>A | p.Pro391His | missense_variant | 9/26 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
L1CAM | ENST00000370060.7 | c.1187C>A | p.Pro396His | missense_variant | 11/29 | 5 | NM_001278116.2 | A1 | |
L1CAM | ENST00000361699.8 | c.1187C>A | p.Pro396His | missense_variant | 10/27 | 1 | P4 | ||
L1CAM | ENST00000361981.7 | c.1172C>A | p.Pro391His | missense_variant | 9/26 | 1 | A1 | ||
L1CAM | ENST00000370055.5 | c.1172C>A | p.Pro391His | missense_variant | 10/27 | 5 | A1 |
Frequencies
GnomAD3 genomes ? Cov.: 24
GnomAD3 exomes AF: 0.00000567 AC: 1AN: 176356Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 62506
GnomAD4 exome Cov.: 33
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 | Jun 08, 2016 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at