rs7052999
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001278116.2(L1CAM):c.3458-34C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0334 in 1,148,254 control chromosomes in the GnomAD database, including 740 homozygotes. There are 11,876 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.052 ( 190 hom., 1608 hem., cov: 23)
Exomes 𝑓: 0.031 ( 550 hom. 10268 hem. )
Consequence
L1CAM
NM_001278116.2 intron
NM_001278116.2 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.0700
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=-0.9).
BP6
?
Variant X-153863583-G-A is Benign according to our data. Variant chrX-153863583-G-A is described in ClinVar as [Benign]. Clinvar id is 256048.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-153863583-G-A is described in Lovd as [Benign].
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.112 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
L1CAM | NM_001278116.2 | c.3458-34C>T | intron_variant | ENST00000370060.7 | |||
L1CAM | NM_000425.5 | c.3458-34C>T | intron_variant | ||||
L1CAM | NM_001143963.2 | c.3443-34C>T | intron_variant | ||||
L1CAM | NM_024003.3 | c.3458-34C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
L1CAM | ENST00000370060.7 | c.3458-34C>T | intron_variant | 5 | NM_001278116.2 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.0519 AC: 5805AN: 111782Hom.: 192 Cov.: 23 AF XY: 0.0469 AC XY: 1594AN XY: 34006
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GnomAD3 exomes AF: 0.0451 AC: 7072AN: 156915Hom.: 214 AF XY: 0.0406 AC XY: 1999AN XY: 49265
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GnomAD4 exome AF: 0.0314 AC: 32559AN: 1036421Hom.: 550 Cov.: 26 AF XY: 0.0329 AC XY: 10268AN XY: 311787
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GnomAD4 genome ? AF: 0.0521 AC: 5822AN: 111833Hom.: 190 Cov.: 23 AF XY: 0.0472 AC XY: 1608AN XY: 34067
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 03, 2015 | - - |
Computational scores
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Name
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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