9-27945981-C-T

Variant names:

• chr9-27945981-C-T
• rs13362909
• NM_001258282.3:c.*2870G>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.*2870G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.12 in 152,044 control chromosomes in the GnomAD database, including 1,815 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 (1815 hom., cov: 32)
• Consequence: LINGO2 NM_001258282.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13
• Publications: 5 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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.27 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINGO2	NM_001258282.3	c.*2870G>A		3_prime_UTR_variant	Exon 7 of 7	ENST00000698399.1	NP_001245211.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINGO2	ENST00000698399.1	c.*2870G>A		3_prime_UTR_variant	Exon 7 of 7		NM_001258282.3	ENSP00000513694.1
LINGO2	ENST00000698405.1	n.624-1044G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.120 AC: 18236 AN: 151926 Hom.: 1806 Cov.: 32

Gnomad AFR AF: 0.275

Gnomad AMI AF: 0.120

Gnomad AMR AF: 0.0725

Gnomad ASJ AF: 0.108

Gnomad EAS AF: 0.0231

Gnomad SAS AF: 0.108

Gnomad FIN AF: 0.0351

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.0592

Gnomad OTH AF: 0.108

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

GnomAD4 genome AF: 0.120 AC: 18279 AN: 152044 Hom.: 1815 Cov.: 32 AF XY: 0.117 AC XY: 8676 AN XY: 74328

African (AFR) AF: 0.275 AC: 11384 AN: 41456

American (AMR) AF: 0.0724 AC: 1106 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.108 AC: 374 AN: 3468

East Asian (EAS) AF: 0.0234 AC: 121 AN: 5172

South Asian (SAS) AF: 0.109 AC: 524 AN: 4818

European-Finnish (FIN) AF: 0.0351 AC: 371 AN: 10564

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.0592 AC: 4023 AN: 67980

Other (OTH) AF: 0.112 AC: 237 AN: 2110

Alfa AF: 0.0696 Hom.: 670

Bravo AF: 0.127

Asia WGS AF: 0.0840 AC: 294 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.24
DANN	Benign	0.62
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs13362909; hg19: chr9-27945979;