NM_001258282.3:c.*3091C>T

Variant names:

• chr9-27945760-G-A
• rs9644872
• NM_001258282.3:c.*3091C>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.*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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0220
• 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=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.567 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.*3091C>T		3_prime_UTR	Exon 7 of 7	NP_001245211.1
	LINGO2	NM_001354574.2		c.*3091C>T		3_prime_UTR	Exon 6 of 6	NP_001341503.1
	LINGO2	NM_001354575.2		c.*3091C>T		3_prime_UTR	Exon 7 of 7	NP_001341504.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINGO2	ENST00000698399.1	MANE Select	c.*3091C>T		3_prime_UTR	Exon 7 of 7	ENSP00000513694.1
	LINGO2	ENST00000698405.1		n.624-823C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.452 AC: 68560 AN: 151702 Hom.: 18347 Cov.: 31

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

African (AFR) AF: 0.154 AC: 6358 AN: 41404

American (AMR) AF: 0.488 AC: 7448 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.503 AC: 1746 AN: 3468

East Asian (EAS) AF: 0.584 AC: 3003 AN: 5142

South Asian (SAS) AF: 0.518 AC: 2497 AN: 4816

European-Finnish (FIN) AF: 0.709 AC: 7497 AN: 10570

Middle Eastern (MID) AF: 0.398 AC: 117 AN: 294

European-Non Finnish (NFE) AF: 0.566 AC: 38378 AN: 67854

Other (OTH) AF: 0.469 AC: 988 AN: 2106

Alfa AF: 0.529 Hom.: 94297

Bravo AF: 0.427

Asia WGS AF: 0.505 AC: 1754 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.6
DANN	Benign	0.52
PhyloP100		-0.022

Splicing

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

Other links and lift over

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