9-28876160-C-T

Variant names:

• chr9-28876160-C-T
• rs16913782
• NM_001258282.3:c.-395+71658G>A

Variant summary

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

The NM_001258282.3(LINGO2):​c.-395+71658G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.137 in 151,848 control chromosomes in the GnomAD database, including 2,027 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 0.14 (2027 hom., cov: 32)
• Consequence: LINGO2 NM_001258282.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.538
• Publications: 2 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=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.271 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINGO2	NM_001258282.3	MANE Select	c.-395+71658G>A		intron	N/A	NP_001245211.1	Q7L985
	LINGO2	NM_001354574.2		c.-362+71658G>A		intron	N/A	NP_001341503.1	Q7L985
	LINGO2	NM_001354575.2		c.-395+71658G>A		intron	N/A	NP_001341504.1	Q7L985

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINGO2	ENST00000698399.1	MANE Select	c.-395+71658G>A		intron	N/A	ENSP00000513694.1	Q7L985
	LINGO2	ENST00000698401.1		c.-765+71658G>A		intron	N/A	ENSP00000513696.1	Q7L985
	LINGO2	ENST00000698402.1		c.-550+71658G>A		intron	N/A	ENSP00000513697.1	Q7L985

Frequencies

GnomAD3 genomes AF: 0.137 AC: 20740 AN: 151730 Hom.: 2028 Cov.: 32

Gnomad AFR AF: 0.276

Gnomad AMI AF: 0.0110

Gnomad AMR AF: 0.0999

Gnomad ASJ AF: 0.0695

Gnomad EAS AF: 0.105

Gnomad SAS AF: 0.0956

Gnomad FIN AF: 0.0982

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.0773

Gnomad OTH AF: 0.118

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

GnomAD4 genome AF: 0.137 AC: 20757 AN: 151848 Hom.: 2027 Cov.: 32 AF XY: 0.136 AC XY: 10127 AN XY: 74224

African (AFR) AF: 0.275 AC: 11398 AN: 41412

American (AMR) AF: 0.100 AC: 1523 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.0695 AC: 241 AN: 3466

East Asian (EAS) AF: 0.105 AC: 545 AN: 5178

South Asian (SAS) AF: 0.0957 AC: 461 AN: 4816

European-Finnish (FIN) AF: 0.0982 AC: 1032 AN: 10508

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.0774 AC: 5254 AN: 67924

Other (OTH) AF: 0.116 AC: 245 AN: 2108

Alfa AF: 0.0790 Hom.: 166

Bravo AF: 0.142

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	3.4
DANN	Benign	0.73
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs16913782; hg19: chr9-28876158;