9-27949699-C-G
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_001258282.3(LINGO2):c.973G>C(p.Val325Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000477 in 1,614,098 control chromosomes in the GnomAD database, including 7 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0025 ( 2 hom., cov: 32)
Exomes 𝑓: 0.00026 ( 5 hom. )
Consequence
LINGO2
NM_001258282.3 missense
NM_001258282.3 missense
Scores
1
1
15
Clinical Significance
Conservation
PhyloP100: 2.61
Genes affected
LINGO2 (HGNC:21207): (leucine rich repeat and Ig domain containing 2) Predicted to act upstream of or within positive regulation of synapse assembly. Predicted to be integral component of membrane. Predicted to be active in extracellular matrix and extracellular space. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.010600269).
BP6
?
Variant 9-27949699-C-G is Benign according to our data. Variant chr9-27949699-C-G is described in ClinVar as [Benign]. Clinvar id is 725600.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
?
High AC in GnomAd at 386 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LINGO2 | NM_001258282.3 | c.973G>C | p.Val325Leu | missense_variant | 7/7 | ENST00000698399.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LINGO2 | ENST00000698399.1 | c.973G>C | p.Val325Leu | missense_variant | 7/7 | NM_001258282.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00254 AC: 386AN: 152148Hom.: 2 Cov.: 32
GnomAD3 genomes
?
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GnomAD3 exomes AF: 0.000678 AC: 170AN: 250910Hom.: 2 AF XY: 0.000531 AC XY: 72AN XY: 135574
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GnomAD4 exome AF: 0.000263 AC: 385AN: 1461832Hom.: 5 Cov.: 33 AF XY: 0.000227 AC XY: 165AN XY: 727220
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GnomAD4 genome ? AF: 0.00253 AC: 385AN: 152266Hom.: 2 Cov.: 32 AF XY: 0.00253 AC XY: 188AN XY: 74432
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 13, 2017 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
DEOGEN2
Benign
T;T;T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
MetaRNN
Benign
T;T;T
MetaSVM
Benign
T
MutationAssessor
Benign
N;N;N
MutationTaster
Benign
D;D
PrimateAI
Pathogenic
D
PROVEAN
Benign
N;N;.
REVEL
Benign
Sift
Benign
T;T;.
Sift4G
Benign
T;T;T
Polyphen
B;B;B
Vest4
MutPred
Gain of sheet (P = 0.1208);Gain of sheet (P = 0.1208);Gain of sheet (P = 0.1208);
MVP
MPC
ClinPred
T
GERP RS
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Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at