rs201151358
Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4BP6_Very_StrongBS1BS2
The NM_001278116.2(L1CAM):c.113C>T(p.Thr38Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00057 in 1,206,671 control chromosomes in the GnomAD database, including 1 homozygotes. There are 220 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. T38T) has been classified as Likely benign.
Frequency
Consequence
NM_001278116.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -17 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
L1CAM | NM_001278116.2 | c.113C>T | p.Thr38Met | missense_variant | 4/29 | ENST00000370060.7 | |
L1CAM | NM_000425.5 | c.113C>T | p.Thr38Met | missense_variant | 3/28 | ||
L1CAM | NM_024003.3 | c.113C>T | p.Thr38Met | missense_variant | 3/27 | ||
L1CAM | NM_001143963.2 | c.98C>T | p.Thr33Met | missense_variant | 2/26 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
L1CAM | ENST00000370060.7 | c.113C>T | p.Thr38Met | missense_variant | 4/29 | 5 | NM_001278116.2 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.000261 AC: 29AN: 111173Hom.: 0 Cov.: 22 AF XY: 0.000240 AC XY: 8AN XY: 33357
GnomAD3 exomes AF: 0.000251 AC: 46AN: 183381Hom.: 1 AF XY: 0.000251 AC XY: 17AN XY: 67833
GnomAD4 exome AF: 0.000602 AC: 659AN: 1095498Hom.: 1 Cov.: 30 AF XY: 0.000587 AC XY: 212AN XY: 360902
GnomAD4 genome ? AF: 0.000261 AC: 29AN: 111173Hom.: 0 Cov.: 22 AF XY: 0.000240 AC XY: 8AN XY: 33357
ClinVar
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Apr 05, 2021 | - - |
Spastic paraplegia Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 02, 2024 | - - |
Inborn genetic diseases Benign:1
Benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 06, 2017 | This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
X-linked hydrocephalus syndrome;C0795953:MASA syndrome;C1839909:X-linked complicated corpus callosum dysgenesis Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Jul 06, 2021 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Sep 10, 2018 | This variant is associated with the following publications: (PMID: 26891472, 19846429) - |
L1CAM-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Dec 29, 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