rs9644872

Variant summary

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

The NM_001258282.3(LINGO2):​c.*3091C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.452 in 151,820 control chromosomes in the GnomAD database, including 18,347 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 0.45 ( 18347 hom., cov: 31)

Consequence

LINGO2
NM_001258282.3 3_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0220
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=-0.83).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.567 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
LINGO2NM_001258282.3 linkuse as main transcriptc.*3091C>T 3_prime_UTR_variant 7/7 ENST00000698399.1 NP_001245211.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
LINGO2ENST00000698399.1 linkuse as main transcriptc.*3091C>T 3_prime_UTR_variant 7/7 NM_001258282.3 ENSP00000513694 P1
LINGO2ENST00000698405.1 linkuse as main transcriptn.624-823C>T intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.452
AC:
68560
AN:
151702
Hom.:
18347
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.154
Gnomad AMI
AF:
0.593
Gnomad AMR
AF:
0.488
Gnomad ASJ
AF:
0.503
Gnomad EAS
AF:
0.584
Gnomad SAS
AF:
0.520
Gnomad FIN
AF:
0.709
Gnomad MID
AF:
0.405
Gnomad NFE
AF:
0.566
Gnomad OTH
AF:
0.470
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.452
AC:
68570
AN:
151820
Hom.:
18347
Cov.:
31
AF XY:
0.461
AC XY:
34194
AN XY:
74200
show subpopulations
Gnomad4 AFR
AF:
0.154
Gnomad4 AMR
AF:
0.488
Gnomad4 ASJ
AF:
0.503
Gnomad4 EAS
AF:
0.584
Gnomad4 SAS
AF:
0.518
Gnomad4 FIN
AF:
0.709
Gnomad4 NFE
AF:
0.566
Gnomad4 OTH
AF:
0.469
Alfa
AF:
0.543
Hom.:
45896
Bravo
AF:
0.427
Asia WGS
AF:
0.505
AC:
1754
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.83
CADD
Benign
1.6
DANN
Benign
0.52

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: rs9644872; hg19: chr9-27945758; COSMIC: COSV58063558; API