NM_001258282.3:c.-314+82204C>T

Variant names:

• chr9-28587996-G-A
• rs2891316
• NM_001258282.3:c.-314+82204C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001258282.3(LINGO2):​c.-314+82204C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.156 in 151,962 control chromosomes in the GnomAD database, including 2,272 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 0.16 (2272 hom., cov: 32)
• Consequence: LINGO2 NM_001258282.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00100
• Publications: 6 publications found

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]

LOC105376004 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 = 0.27 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001258282.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINGO2	NM_001258282.3	MANE Select	c.-314+82204C>T		intron	N/A	NP_001245211.1
	LINGO2	NM_001354574.2		c.-281+82204C>T		intron	N/A	NP_001341503.1
	LINGO2	NM_001354575.2		c.-314+82204C>T		intron	N/A	NP_001341504.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINGO2	ENST00000698399.1	MANE Select	c.-314+82204C>T		intron	N/A	ENSP00000513694.1
	LINGO2	ENST00000379992.6	TSL:5	c.-365+82204C>T		intron	N/A	ENSP00000369328.1
	LINGO2	ENST00000698400.1		c.-529+82204C>T		intron	N/A	ENSP00000513695.1

Frequencies

GnomAD3 genomes AF: 0.156 AC: 23724 AN: 151842 Hom.: 2268 Cov.: 32

Gnomad AFR AF: 0.0765

Gnomad AMI AF: 0.368

Gnomad AMR AF: 0.277

Gnomad ASJ AF: 0.261

Gnomad EAS AF: 0.0228

Gnomad SAS AF: 0.120

Gnomad FIN AF: 0.157

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.181

Gnomad OTH AF: 0.183

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.156 AC: 23733 AN: 151962 Hom.: 2272 Cov.: 32 AF XY: 0.157 AC XY: 11686 AN XY: 74272

African (AFR) AF: 0.0766 AC: 3179 AN: 41482

American (AMR) AF: 0.277 AC: 4214 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.261 AC: 905 AN: 3468

East Asian (EAS) AF: 0.0226 AC: 116 AN: 5126

South Asian (SAS) AF: 0.120 AC: 576 AN: 4814

European-Finnish (FIN) AF: 0.157 AC: 1660 AN: 10598

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.181 AC: 12302 AN: 67920

Other (OTH) AF: 0.181 AC: 383 AN: 2112

Alfa AF: 0.181 Hom.: 2561

Bravo AF: 0.165

Asia WGS AF: 0.0910 AC: 316 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.9
DANN	Benign	0.56
PhyloP100		0.0010
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2891316; hg19: chr9-28587994;