chrX-153862663-C-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4_ModerateBP6_ModerateBP7
The NM_001278116.2(L1CAM):c.3774G>A(p.Ter1258=) variant causes a stop retained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000147 in 1,089,473 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 7 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 stop_retained
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
L1CAM | NM_001278116.2 | c.3774G>A | p.Ter1258= | stop_retained_variant | 29/29 | ENST00000370060.7 | |
L1CAM | NM_000425.5 | c.3774G>A | p.Ter1258= | stop_retained_variant | 28/28 | ||
L1CAM | NM_024003.3 | c.3762G>A | p.Ter1254= | stop_retained_variant | 27/27 | ||
L1CAM | NM_001143963.2 | c.3747G>A | p.Ter1249= | stop_retained_variant | 26/26 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
L1CAM | ENST00000370060.7 | c.3774G>A | p.Ter1258= | stop_retained_variant | 29/29 | 5 | NM_001278116.2 | A1 |
Frequencies
GnomAD3 genomes ? Cov.: 24
GnomAD3 exomes AF: 0.00000560 AC: 1AN: 178555Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 63695
GnomAD4 exome AF: 0.0000147 AC: 16AN: 1089473Hom.: 0 Cov.: 28 AF XY: 0.0000197 AC XY: 7AN XY: 355687
GnomAD4 genome ? Cov.: 24
ClinVar
Submissions by phenotype
Spastic paraplegia Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jun 02, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at