rs202082978
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BS1BS2
The NM_001278116.2(L1CAM):c.3015C>T(p.Ile1005Ile) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000841 in 1,211,194 control chromosomes in the GnomAD database, including 8 homozygotes. There are 582 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 -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
L1CAM | NM_001278116.2 | c.3015C>T | p.Ile1005Ile | synonymous_variant | 23/29 | ENST00000370060.7 | NP_001265045.1 | |
L1CAM | NM_000425.5 | c.3015C>T | p.Ile1005Ile | synonymous_variant | 22/28 | NP_000416.1 | ||
L1CAM | NM_024003.3 | c.3015C>T | p.Ile1005Ile | synonymous_variant | 22/27 | NP_076493.1 | ||
L1CAM | NM_001143963.2 | c.3000C>T | p.Ile1000Ile | synonymous_variant | 21/26 | NP_001137435.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
L1CAM | ENST00000370060.7 | c.3015C>T | p.Ile1005Ile | synonymous_variant | 23/29 | 5 | NM_001278116.2 | ENSP00000359077.1 | ||
L1CAM | ENST00000361699.8 | c.3015C>T | p.Ile1005Ile | synonymous_variant | 22/27 | 1 | ENSP00000355380.4 | |||
L1CAM | ENST00000361981.7 | c.3000C>T | p.Ile1000Ile | synonymous_variant | 21/26 | 1 | ENSP00000354712.3 | |||
L1CAM | ENST00000370055.5 | c.3000C>T | p.Ile1000Ile | synonymous_variant | 22/27 | 5 | ENSP00000359072.1 |
Frequencies
GnomAD3 genomes AF: 0.000372 AC: 42AN: 112971Hom.: 1 Cov.: 24 AF XY: 0.000598 AC XY: 21AN XY: 35119
GnomAD3 exomes AF: 0.00179 AC: 328AN: 183447Hom.: 3 AF XY: 0.00298 AC XY: 202AN XY: 67891
GnomAD4 exome AF: 0.000891 AC: 978AN: 1098171Hom.: 7 Cov.: 33 AF XY: 0.00154 AC XY: 561AN XY: 363531
GnomAD4 genome AF: 0.000363 AC: 41AN: 113023Hom.: 1 Cov.: 24 AF XY: 0.000597 AC XY: 21AN XY: 35181
ClinVar
Submissions by phenotype
not specified Uncertain:1Benign:1
Benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Feb 27, 2015 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Feb 26, 2015 | - - |
Spastic paraplegia Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 28, 2024 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Feb 06, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at