9-28719761-G-C

Variant names:

• chr9-28719761-G-C
• rs6476092
• NM_001258282.3:c.-394-49481C>G

Variant summary

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

The NM_001258282.3(LINGO2):​c.-394-49481C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.242 in 151,720 control chromosomes in the GnomAD database, including 4,859 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 0.24 (4859 hom., cov: 32)
• Consequence: LINGO2 NM_001258282.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0580
• 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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.369 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.-394-49481C>G		intron	N/A	NP_001245211.1
	LINGO2	NM_001354574.2		c.-361-49481C>G		intron	N/A	NP_001341503.1
	LINGO2	NM_001354575.2		c.-394-49481C>G		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.-394-49481C>G		intron	N/A	ENSP00000513694.1
	LINGO2	ENST00000698401.1		c.-764-49481C>G		intron	N/A	ENSP00000513696.1
	LINGO2	ENST00000698402.1		c.-549-49481C>G		intron	N/A	ENSP00000513697.1

Frequencies

GnomAD3 genomes AF: 0.243 AC: 36781 AN: 151606 Hom.: 4863 Cov.: 32

Gnomad AFR AF: 0.154

Gnomad AMI AF: 0.186

Gnomad AMR AF: 0.377

Gnomad ASJ AF: 0.166

Gnomad EAS AF: 0.288

Gnomad SAS AF: 0.269

Gnomad FIN AF: 0.325

Gnomad MID AF: 0.201

Gnomad NFE AF: 0.253

Gnomad OTH AF: 0.265

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

GnomAD4 genome AF: 0.242 AC: 36779 AN: 151720 Hom.: 4859 Cov.: 32 AF XY: 0.250 AC XY: 18495 AN XY: 74112

African (AFR) AF: 0.154 AC: 6356 AN: 41396

American (AMR) AF: 0.377 AC: 5733 AN: 15208

Ashkenazi Jewish (ASJ) AF: 0.166 AC: 574 AN: 3466

East Asian (EAS) AF: 0.288 AC: 1482 AN: 5146

South Asian (SAS) AF: 0.270 AC: 1297 AN: 4812

European-Finnish (FIN) AF: 0.325 AC: 3421 AN: 10516

Middle Eastern (MID) AF: 0.192 AC: 56 AN: 292

European-Non Finnish (NFE) AF: 0.253 AC: 17139 AN: 67872

Other (OTH) AF: 0.262 AC: 551 AN: 2100

Alfa AF: 0.133 Hom.: 277

Bravo AF: 0.242

Asia WGS AF: 0.290 AC: 1006 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.1
DANN	Benign	0.80
PhyloP100		-0.058

Splicing

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

Other links and lift over

dbSNP: rs6476092; hg19: chr9-28719759;