rs7856324

Variant names:

• chr9-28366645-G-A
• rs7856324
• NM_001258282.3:c.-195+6191C>T

Your query was ambiguous. Multiple possible variants found:

• chr9-28366645-G-A
• chr9-28366645-G-C
• chr9-28366645-G-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.-195+6191C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.117 in 149,842 control chromosomes in the GnomAD database, including 1,170 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 0.12 (1170 hom., cov: 32)
• Consequence: LINGO2 NM_001258282.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.433
• 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.155 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.-195+6191C>T		intron	N/A	NP_001245211.1	Q7L985
	LINGO2	NM_001354574.2		c.-194-71279C>T		intron	N/A	NP_001341503.1	Q7L985
	LINGO2	NM_001354575.2		c.-195+6191C>T		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.-195+6191C>T		intron	N/A	ENSP00000513694.1	Q7L985
	LINGO2	ENST00000379992.6	TSL:5	c.-246+6191C>T		intron	N/A	ENSP00000369328.1	Q7L985
	LINGO2	ENST00000698400.1		c.-410+6191C>T		intron	N/A	ENSP00000513695.1	Q7L985

Frequencies

GnomAD3 genomes AF: 0.117 AC: 17592 AN: 149738 Hom.: 1170 Cov.: 32

Gnomad AFR AF: 0.158

Gnomad AMI AF: 0.0453

Gnomad AMR AF: 0.0821

Gnomad ASJ AF: 0.104

Gnomad EAS AF: 0.159

Gnomad SAS AF: 0.106

Gnomad FIN AF: 0.0718

Gnomad MID AF: 0.0784

Gnomad NFE AF: 0.108

Gnomad OTH AF: 0.100

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

GnomAD4 genome AF: 0.117 AC: 17596 AN: 149842 Hom.: 1170 Cov.: 32 AF XY: 0.114 AC XY: 8349 AN XY: 73104

African (AFR) AF: 0.158 AC: 6428 AN: 40754

American (AMR) AF: 0.0822 AC: 1239 AN: 15080

Ashkenazi Jewish (ASJ) AF: 0.104 AC: 358 AN: 3442

East Asian (EAS) AF: 0.159 AC: 806 AN: 5074

South Asian (SAS) AF: 0.105 AC: 495 AN: 4694

European-Finnish (FIN) AF: 0.0718 AC: 732 AN: 10194

Middle Eastern (MID) AF: 0.0674 AC: 19 AN: 282

European-Non Finnish (NFE) AF: 0.108 AC: 7270 AN: 67340

Other (OTH) AF: 0.100 AC: 208 AN: 2076

Alfa AF: 0.101 Hom.: 1402

Bravo AF: 0.118

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.43
DANN	Benign	0.14
PhyloP100		-0.43
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: rs7856324; hg19: chr9-28366643;