rs782756293
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 2P and 8B. PM1BP6_Very_Strong
The NM_001278116.2(L1CAM):c.1219C>T(p.Arg407Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000547 in 1,096,695 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 2 hemizygotes in GnomAD. 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. R407H) has been classified as Likely benign.
Frequency
Consequence
NM_001278116.2 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
L1CAM | NM_001278116.2 | c.1219C>T | p.Arg407Cys | missense_variant | 11/29 | ENST00000370060.7 | |
L1CAM | NM_000425.5 | c.1219C>T | p.Arg407Cys | missense_variant | 10/28 | ||
L1CAM | NM_024003.3 | c.1219C>T | p.Arg407Cys | missense_variant | 10/27 | ||
L1CAM | NM_001143963.2 | c.1204C>T | p.Arg402Cys | missense_variant | 9/26 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
L1CAM | ENST00000370060.7 | c.1219C>T | p.Arg407Cys | missense_variant | 11/29 | 5 | NM_001278116.2 | A1 | |
L1CAM | ENST00000361699.8 | c.1219C>T | p.Arg407Cys | missense_variant | 10/27 | 1 | P4 | ||
L1CAM | ENST00000361981.7 | c.1204C>T | p.Arg402Cys | missense_variant | 9/26 | 1 | A1 | ||
L1CAM | ENST00000370055.5 | c.1204C>T | p.Arg402Cys | missense_variant | 10/27 | 5 | A1 |
Frequencies
GnomAD3 genomes ? Cov.: 25
GnomAD3 exomes AF: 0.0000224 AC: 4AN: 178588Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 64496
GnomAD4 exome AF: 0.00000547 AC: 6AN: 1096695Hom.: 0 Cov.: 33 AF XY: 0.00000552 AC XY: 2AN XY: 362357
GnomAD4 genome ? Cov.: 25
ClinVar
Submissions by phenotype
Spastic paraplegia Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Aug 02, 2023 | - - |
L1CAM-related condition Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Aug 02, 2023 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at