rs139393266
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_001278116.2(L1CAM):c.3081G>T(p.Ala1027Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0001 in 1,210,385 control chromosomes in the GnomAD database, including 2 homozygotes. There are 58 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.000018 ( 0 hom., 1 hem., cov: 24)
Exomes 𝑓: 0.00011 ( 2 hom. 57 hem. )
Consequence
L1CAM
NM_001278116.2 synonymous
NM_001278116.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -2.34
Genes affected
L1CAM (HGNC:6470): (L1 cell adhesion molecule) The protein encoded by this gene is an axonal glycoprotein belonging to the immunoglobulin supergene family. The ectodomain, consisting of several immunoglobulin-like domains and fibronectin-like repeats (type III), is linked via a single transmembrane sequence to a conserved cytoplasmic domain. This cell adhesion molecule plays an important role in nervous system development, including neuronal migration and differentiation. Mutations in the gene cause X-linked neurological syndromes known as CRASH (corpus callosum hypoplasia, retardation, aphasia, spastic paraplegia and hydrocephalus). Alternative splicing of this gene results in multiple transcript variants, some of which include an alternate exon that is considered to be specific to neurons. [provided by RefSeq, May 2013]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -21 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.58).
BP6
Variant X-153864670-C-A is Benign according to our data. Variant chrX-153864670-C-A is described in ClinVar as [Likely_benign]. Clinvar id is 668994.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-153864670-C-A is described in Lovd as [Likely_benign].
BP7
Synonymous conserved (PhyloP=-2.34 with no splicing effect.
BS1
Variant frequency is greater than expected in population sas. gnomad4_exome allele frequency = 0.000108 (119/1098043) while in subpopulation SAS AF= 0.00209 (113/54146). AF 95% confidence interval is 0.00177. There are 2 homozygotes in gnomad4_exome. There are 57 alleles in male gnomad4_exome subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
High Homozygotes in GnomAdExome4 at 2 XL gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
L1CAM | NM_001278116.2 | c.3081G>T | p.Ala1027Ala | synonymous_variant | 24/29 | ENST00000370060.7 | NP_001265045.1 | |
L1CAM | NM_000425.5 | c.3081G>T | p.Ala1027Ala | synonymous_variant | 23/28 | NP_000416.1 | ||
L1CAM | NM_024003.3 | c.3081G>T | p.Ala1027Ala | synonymous_variant | 23/27 | NP_076493.1 | ||
L1CAM | NM_001143963.2 | c.3066G>T | p.Ala1022Ala | synonymous_variant | 22/26 | NP_001137435.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
L1CAM | ENST00000370060.7 | c.3081G>T | p.Ala1027Ala | synonymous_variant | 24/29 | 5 | NM_001278116.2 | ENSP00000359077.1 | ||
L1CAM | ENST00000361699.8 | c.3081G>T | p.Ala1027Ala | synonymous_variant | 23/27 | 1 | ENSP00000355380.4 | |||
L1CAM | ENST00000361981.7 | c.3066G>T | p.Ala1022Ala | synonymous_variant | 22/26 | 1 | ENSP00000354712.3 | |||
L1CAM | ENST00000370055.5 | c.3066G>T | p.Ala1022Ala | synonymous_variant | 23/27 | 5 | ENSP00000359072.1 |
Frequencies
GnomAD3 genomes AF: 0.0000178 AC: 2AN: 112290Hom.: 0 Cov.: 24 AF XY: 0.0000290 AC XY: 1AN XY: 34458
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GnomAD3 exomes AF: 0.000240 AC: 44AN: 183449Hom.: 1 AF XY: 0.000309 AC XY: 21AN XY: 67883
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GnomAD4 exome AF: 0.000108 AC: 119AN: 1098043Hom.: 2 Cov.: 33 AF XY: 0.000157 AC XY: 57AN XY: 363413
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GnomAD4 genome AF: 0.0000178 AC: 2AN: 112342Hom.: 0 Cov.: 24 AF XY: 0.0000290 AC XY: 1AN XY: 34520
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Spastic paraplegia Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 10, 2024 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 20, 2018 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
L1CAM-related disorder Benign:1
Likely benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | May 30, 2019 | 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
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at