rs201131192
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_001278116.2(L1CAM):āc.1581A>Cā(p.Thr527=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000322 in 1,210,227 control chromosomes in the GnomAD database, including 2 homozygotes. There are 210 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ). Synonymous variant affecting the same amino acid position (i.e. T527T) has been classified as Likely benign.
Frequency
Consequence
NM_001278116.2 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
L1CAM | NM_001278116.2 | c.1581A>C | p.Thr527= | synonymous_variant | 14/29 | ENST00000370060.7 | |
L1CAM | NM_000425.5 | c.1581A>C | p.Thr527= | synonymous_variant | 13/28 | ||
L1CAM | NM_024003.3 | c.1581A>C | p.Thr527= | synonymous_variant | 13/27 | ||
L1CAM | NM_001143963.2 | c.1566A>C | p.Thr522= | synonymous_variant | 12/26 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
L1CAM | ENST00000370060.7 | c.1581A>C | p.Thr527= | synonymous_variant | 14/29 | 5 | NM_001278116.2 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.000143 AC: 16AN: 111945Hom.: 0 Cov.: 24 AF XY: 0.000293 AC XY: 10AN XY: 34125
GnomAD3 exomes AF: 0.000758 AC: 139AN: 183473Hom.: 1 AF XY: 0.000928 AC XY: 63AN XY: 67919
GnomAD4 exome AF: 0.000341 AC: 374AN: 1098227Hom.: 2 Cov.: 33 AF XY: 0.000550 AC XY: 200AN XY: 363589
GnomAD4 genome ? AF: 0.000143 AC: 16AN: 112000Hom.: 0 Cov.: 24 AF XY: 0.000292 AC XY: 10AN XY: 34190
ClinVar
Submissions by phenotype
Spastic paraplegia Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 22, 2024 | - - |
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Jun 24, 2015 | - - |
Inborn genetic diseases Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 22, 2016 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Hereditary spastic paraplegia Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Genome Diagnostics Laboratory, The Hospital for Sick Children | Mar 01, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at