X-153862690-G-T
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_StrongBP6_ModerateBP7
The NM_001278116.2(L1CAM):c.3747C>A(p.Pro1249=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000274 in 1,096,627 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 2 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: not found (cov: 24)
Exomes 𝑓: 0.0000027 ( 0 hom. 2 hem. )
Consequence
L1CAM
NM_001278116.2 synonymous
NM_001278116.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.0800
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 -7 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.58).
BP6
?
Variant X-153862690-G-T is Benign according to our data. Variant chrX-153862690-G-T is described in ClinVar as [Benign]. Clinvar id is 2725540.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=0.08 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
L1CAM | NM_001278116.2 | c.3747C>A | p.Pro1249= | synonymous_variant | 29/29 | ENST00000370060.7 | |
L1CAM | NM_000425.5 | c.3747C>A | p.Pro1249= | synonymous_variant | 28/28 | ||
L1CAM | NM_024003.3 | c.3735C>A | p.Pro1245= | synonymous_variant | 27/27 | ||
L1CAM | NM_001143963.2 | c.3720C>A | p.Pro1240= | synonymous_variant | 26/26 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
L1CAM | ENST00000370060.7 | c.3747C>A | p.Pro1249= | synonymous_variant | 29/29 | 5 | NM_001278116.2 | A1 |
Frequencies
GnomAD3 genomes ? Cov.: 24
GnomAD3 genomes
?
Cov.:
24
GnomAD3 exomes AF: 0.00000551 AC: 1AN: 181379Hom.: 0 AF XY: 0.0000150 AC XY: 1AN XY: 66479
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GnomAD4 exome AF: 0.00000274 AC: 3AN: 1096627Hom.: 0 Cov.: 30 AF XY: 0.00000552 AC XY: 2AN XY: 362063
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GnomAD4 genome ? Cov.: 24
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Spastic paraplegia Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 14, 2024 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at