9-27950619-A-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001258282.3(LINGO2):c.53T>G(p.Val18Gly) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000293 in 1,364,558 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001258282.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LINGO2 | NM_001258282.3 | c.53T>G | p.Val18Gly | missense_variant | 7/7 | ENST00000698399.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LINGO2 | ENST00000698399.1 | c.53T>G | p.Val18Gly | missense_variant | 7/7 | NM_001258282.3 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.0000112 AC: 2AN: 177808Hom.: 0 AF XY: 0.0000107 AC XY: 1AN XY: 93188
GnomAD4 exome AF: 0.00000293 AC: 4AN: 1364558Hom.: 0 Cov.: 31 AF XY: 0.00000449 AC XY: 3AN XY: 667986
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 26, 2023 | The c.53T>G (p.V18G) alteration is located in exon 7 (coding exon 1) of the LINGO2 gene. This alteration results from a T to G substitution at nucleotide position 53, causing the valine (V) at amino acid position 18 to be replaced by a glycine (G). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at