rs200561489
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6BP7BS2
The NM_001278116.2(L1CAM):c.2106G>A(p.Pro702=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000389 in 1,208,385 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 12 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_001278116.2 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
L1CAM | NM_001278116.2 | c.2106G>A | p.Pro702= | synonymous_variant | 17/29 | ENST00000370060.7 | |
L1CAM | NM_000425.5 | c.2106G>A | p.Pro702= | synonymous_variant | 16/28 | ||
L1CAM | NM_024003.3 | c.2106G>A | p.Pro702= | synonymous_variant | 16/27 | ||
L1CAM | NM_001143963.2 | c.2091G>A | p.Pro697= | synonymous_variant | 15/26 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
L1CAM | ENST00000370060.7 | c.2106G>A | p.Pro702= | synonymous_variant | 17/29 | 5 | NM_001278116.2 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000629 AC: 7AN: 111360Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 33538
GnomAD3 exomes AF: 0.0000164 AC: 3AN: 183280Hom.: 0 AF XY: 0.0000147 AC XY: 1AN XY: 67832
GnomAD4 exome AF: 0.0000365 AC: 40AN: 1097025Hom.: 0 Cov.: 31 AF XY: 0.0000331 AC XY: 12AN XY: 362681
GnomAD4 genome ? AF: 0.0000629 AC: 7AN: 111360Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 33538
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Jul 13, 2015 | - - |
Spastic paraplegia Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 18, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at