rs11853548
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_032808.7(LINGO1):c.1575C>T(p.Pro525Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00221 in 1,613,946 control chromosomes in the GnomAD database, including 73 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_032808.7 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LINGO1 | ENST00000355300.7 | c.1575C>T | p.Pro525Pro | synonymous_variant | Exon 2 of 2 | 1 | NM_032808.7 | ENSP00000347451.6 | ||
LINGO1 | ENST00000561030.5 | c.1557C>T | p.Pro519Pro | synonymous_variant | Exon 4 of 4 | 1 | ENSP00000453853.1 |
Frequencies
GnomAD3 genomes AF: 0.0119 AC: 1805AN: 152228Hom.: 33 Cov.: 33
GnomAD3 exomes AF: 0.00315 AC: 783AN: 248782Hom.: 16 AF XY: 0.00241 AC XY: 326AN XY: 134994
GnomAD4 exome AF: 0.00120 AC: 1756AN: 1461600Hom.: 40 Cov.: 31 AF XY: 0.00103 AC XY: 752AN XY: 727078
GnomAD4 genome AF: 0.0119 AC: 1812AN: 152346Hom.: 33 Cov.: 33 AF XY: 0.0113 AC XY: 843AN XY: 74498
ClinVar
Submissions by phenotype
not provided Benign:2
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LINGO1-related disorder Benign:1
This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at