rs11856876
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000561030.5(LINGO1):c.-98-3496T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.404 in 151,754 control chromosomes in the GnomAD database, including 13,143 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.40 ( 13143 hom., cov: 31)
Consequence
LINGO1
ENST00000561030.5 intron
ENST00000561030.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.296
Genes affected
LINGO1 (HGNC:21205): (leucine rich repeat and Ig domain containing 1) Predicted to enable epidermal growth factor receptor binding activity. Predicted to act upstream of or within generation of neurons and protein kinase B signaling. Predicted to be located in plasma membrane. Predicted to be active in extracellular matrix and extracellular space. Implicated in autosomal recessive non-syndromic intellectual disability and glaucoma. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.93).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.548 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LINGO1 | NM_001301186.2 | c.-98-3496T>G | intron_variant | ||||
LINGO1 | NM_001301187.2 | c.-98-3496T>G | intron_variant | ||||
LINGO1 | NM_001301189.2 | c.-98-3496T>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LINGO1 | ENST00000561030.5 | c.-98-3496T>G | intron_variant | 1 | P4 | ||||
LINGO1 | ENST00000559893.5 | c.-98-3496T>G | intron_variant | 4 | |||||
LINGO1 | ENST00000561686.5 | c.-13+10050T>G | intron_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.404 AC: 61282AN: 151636Hom.: 13132 Cov.: 31
GnomAD3 genomes
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31
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.404 AC: 61337AN: 151754Hom.: 13143 Cov.: 31 AF XY: 0.406 AC XY: 30111AN XY: 74164
GnomAD4 genome
?
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61337
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31
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30111
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74164
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1406
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at