NM_001278116.2:c.3764C>T
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_ModerateBP6_ModerateBS1BS2
The NM_001278116.2(L1CAM):c.3764C>T(p.Ala1255Val) variant causes a missense change. The variant allele was found at a frequency of 0.00000746 in 1,206,987 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 5 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A1255T) has been classified as Benign.
Frequency
Consequence
NM_001278116.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
L1CAM | NM_001278116.2 | c.3764C>T | p.Ala1255Val | missense_variant | Exon 29 of 29 | ENST00000370060.7 | NP_001265045.1 | |
L1CAM | NM_000425.5 | c.3764C>T | p.Ala1255Val | missense_variant | Exon 28 of 28 | NP_000416.1 | ||
L1CAM | NM_024003.3 | c.3752C>T | p.Ala1251Val | missense_variant | Exon 27 of 27 | NP_076493.1 | ||
L1CAM | NM_001143963.2 | c.3737C>T | p.Ala1246Val | missense_variant | Exon 26 of 26 | NP_001137435.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000177 AC: 2AN: 112828Hom.: 0 Cov.: 24 AF XY: 0.0000286 AC XY: 1AN XY: 34984
GnomAD3 exomes AF: 0.0000388 AC: 7AN: 180201Hom.: 0 AF XY: 0.0000613 AC XY: 4AN XY: 65241
GnomAD4 exome AF: 0.00000640 AC: 7AN: 1094159Hom.: 0 Cov.: 29 AF XY: 0.0000111 AC XY: 4AN XY: 359805
GnomAD4 genome AF: 0.0000177 AC: 2AN: 112828Hom.: 0 Cov.: 24 AF XY: 0.0000286 AC XY: 1AN XY: 34984
ClinVar
Submissions by phenotype
Spastic paraplegia Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at