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GeneBe

9-28983840-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001258282.3(LINGO2):c.-491-35926G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.65 in 151,642 control chromosomes in the GnomAD database, including 32,648 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 0.65 ( 32648 hom., cov: 31)

Consequence

LINGO2
NM_001258282.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0460
Variant links:
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 -12 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.93).
BA1
?
    BA1 - Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.712 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
LINGO2NM_001258282.3 linkuse as main transcriptc.-491-35926G>A intron_variant ENST00000698399.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
LINGO2ENST00000698399.1 linkuse as main transcriptc.-491-35926G>A intron_variant NM_001258282.3 P1
LINGO2ENST00000698401.1 linkuse as main transcriptc.-861-35926G>A intron_variant P1
LINGO2ENST00000698402.1 linkuse as main transcriptc.-646-35926G>A intron_variant P1
LINGO2ENST00000698404.1 linkuse as main transcriptc.-602-35926G>A intron_variant

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.651
AC:
98573
AN:
151524
Hom.:
32633
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.514
Gnomad AMI
AF:
0.576
Gnomad AMR
AF:
0.669
Gnomad ASJ
AF:
0.796
Gnomad EAS
AF:
0.585
Gnomad SAS
AF:
0.635
Gnomad FIN
AF:
0.724
Gnomad MID
AF:
0.687
Gnomad NFE
AF:
0.717
Gnomad OTH
AF:
0.671
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.650
AC:
98634
AN:
151642
Hom.:
32648
Cov.:
31
AF XY:
0.649
AC XY:
48102
AN XY:
74094
show subpopulations
Gnomad4 AFR
AF:
0.514
Gnomad4 AMR
AF:
0.669
Gnomad4 ASJ
AF:
0.796
Gnomad4 EAS
AF:
0.585
Gnomad4 SAS
AF:
0.636
Gnomad4 FIN
AF:
0.724
Gnomad4 NFE
AF:
0.717
Gnomad4 OTH
AF:
0.666
Alfa
AF:
0.595
Hom.:
1792
Bravo
AF:
0.640
Asia WGS
AF:
0.588
AC:
2043
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.93
Cadd
Benign
0.99
Dann
Benign
0.37

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1813345; hg19: chr9-28983838; API