chrX-153864303-C-T
Variant summary
Our verdict is Benign. The variant received -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_001278116.2(L1CAM):c.3322+19G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000158 in 1,205,574 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 8 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_001278116.2 intron
Scores
Clinical Significance
Conservation
Publications
- L1 syndromeInheritance: XL Classification: DEFINITIVE Submitted by: ClinGen
- X-linked hydrocephalus with stenosis of the aqueduct of SylviusInheritance: XL Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Genomics England PanelApp, Orphanet, G2P
- MASA syndromeInheritance: XL Classification: STRONG, SUPPORTIVE Submitted by: Genomics England PanelApp, Orphanet
- X-linked complicated corpus callosum dysgenesisInheritance: XL Classification: STRONG, SUPPORTIVE Submitted by: Orphanet, Genomics England PanelApp, Labcorp Genetics (formerly Invitae)
- X-linked complicated spastic paraplegia type 1Inheritance: XL Classification: SUPPORTIVE Submitted by: Orphanet
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ACMG classification
Our verdict: Benign. The variant received -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
L1CAM | NM_001278116.2 | c.3322+19G>A | intron_variant | Intron 25 of 28 | ENST00000370060.7 | NP_001265045.1 | ||
L1CAM | NM_000425.5 | c.3322+19G>A | intron_variant | Intron 24 of 27 | NP_000416.1 | |||
L1CAM | NM_024003.3 | c.3322+19G>A | intron_variant | Intron 24 of 26 | NP_076493.1 | |||
L1CAM | NM_001143963.2 | c.3307+19G>A | intron_variant | Intron 23 of 25 | NP_001137435.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000178 AC: 2AN: 112345Hom.: 0 Cov.: 24 show subpopulations
GnomAD2 exomes AF: 0.0000276 AC: 5AN: 181277 AF XY: 0.0000302 show subpopulations
GnomAD4 exome AF: 0.0000156 AC: 17AN: 1093229Hom.: 0 Cov.: 31 AF XY: 0.0000195 AC XY: 7AN XY: 359379 show subpopulations
Age Distribution
GnomAD4 genome AF: 0.0000178 AC: 2AN: 112345Hom.: 0 Cov.: 24 AF XY: 0.0000290 AC XY: 1AN XY: 34515 show subpopulations
ClinVar
Submissions by phenotype
not specified Benign:2
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. -
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Spastic paraplegia Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at