rs140240430
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_001278116.2(L1CAM):c.1704-14C>T variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00265 in 1,208,061 control chromosomes in the GnomAD database, including 50 homozygotes. There are 867 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.014 ( 34 hom., 409 hem., cov: 23)
Exomes 𝑓: 0.0015 ( 16 hom. 458 hem. )
Consequence
L1CAM
NM_001278116.2 splice_polypyrimidine_tract, intron
NM_001278116.2 splice_polypyrimidine_tract, intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.903
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 -20 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.96).
BP6
?
Variant X-153868136-G-A is Benign according to our data. Variant chrX-153868136-G-A is described in ClinVar as [Benign]. Clinvar id is 92919.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0139 (1548/111518) while in subpopulation AFR AF= 0.0476 (1459/30667). AF 95% confidence interval is 0.0455. There are 34 homozygotes in gnomad4. There are 409 alleles in male gnomad4 subpopulation. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 34 XL gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
L1CAM | NM_001278116.2 | c.1704-14C>T | splice_polypyrimidine_tract_variant, intron_variant | ENST00000370060.7 | |||
L1CAM | NM_000425.5 | c.1704-14C>T | splice_polypyrimidine_tract_variant, intron_variant | ||||
L1CAM | NM_001143963.2 | c.1689-14C>T | splice_polypyrimidine_tract_variant, intron_variant | ||||
L1CAM | NM_024003.3 | c.1704-14C>T | splice_polypyrimidine_tract_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
L1CAM | ENST00000370060.7 | c.1704-14C>T | splice_polypyrimidine_tract_variant, intron_variant | 5 | NM_001278116.2 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.0138 AC: 1543AN: 111466Hom.: 34 Cov.: 23 AF XY: 0.0121 AC XY: 407AN XY: 33648
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GnomAD3 exomes AF: 0.00396 AC: 718AN: 181159Hom.: 16 AF XY: 0.00247 AC XY: 163AN XY: 65999
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GnomAD4 exome AF: 0.00151 AC: 1654AN: 1096543Hom.: 16 Cov.: 32 AF XY: 0.00126 AC XY: 458AN XY: 362253
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GnomAD4 genome ? AF: 0.0139 AC: 1548AN: 111518Hom.: 34 Cov.: 23 AF XY: 0.0121 AC XY: 409AN XY: 33710
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ClinVar
Significance: Benign
Submissions summary: Benign:5
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:3
Benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Aug 01, 2013 | - - |
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Nov 18, 2013 | - - |
Spastic paraplegia Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 03, 2015 | - - |
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