chr9-28025179-C-G

Variant summary

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

The NM_001258282.3(LINGO2):​c.-35-74473G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.62 in 152,000 control chromosomes in the GnomAD database, including 30,153 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 0.62 ( 30153 hom., cov: 32)

Consequence

LINGO2
NM_001258282.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.377
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
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.737 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
LINGO2NM_001258282.3 linkuse as main transcriptc.-35-74473G>C intron_variant ENST00000698399.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
LINGO2ENST00000698399.1 linkuse as main transcriptc.-35-74473G>C intron_variant NM_001258282.3 P1

Frequencies

GnomAD3 genomes
AF:
0.620
AC:
94152
AN:
151882
Hom.:
30148
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.451
Gnomad AMI
AF:
0.840
Gnomad AMR
AF:
0.748
Gnomad ASJ
AF:
0.736
Gnomad EAS
AF:
0.467
Gnomad SAS
AF:
0.597
Gnomad FIN
AF:
0.630
Gnomad MID
AF:
0.715
Gnomad NFE
AF:
0.695
Gnomad OTH
AF:
0.667
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.620
AC:
94192
AN:
152000
Hom.:
30153
Cov.:
32
AF XY:
0.619
AC XY:
45984
AN XY:
74250
show subpopulations
Gnomad4 AFR
AF:
0.451
Gnomad4 AMR
AF:
0.748
Gnomad4 ASJ
AF:
0.736
Gnomad4 EAS
AF:
0.467
Gnomad4 SAS
AF:
0.596
Gnomad4 FIN
AF:
0.630
Gnomad4 NFE
AF:
0.695
Gnomad4 OTH
AF:
0.664
Alfa
AF:
0.639
Hom.:
3948
Bravo
AF:
0.622
Asia WGS
AF:
0.542
AC:
1889
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
CADD
Benign
1.1
DANN
Benign
0.51

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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: rs944648; hg19: chr9-28025177; API