rs10968215

chr9-27940162-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001258282.3(LINGO2):c.*8689G>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 0.282 in 151,620 control chromosomes in the GnomAD database, including 6,528 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 0.28 (6528 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: LINGO2 NM_001258282.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.184

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.406 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINGO2	NM_001258282.3	c.*8689G>A		3_prime_UTR_variant	7/7	ENST00000698399.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINGO2	ENST00000698399.1	c.*8689G>A		3_prime_UTR_variant	7/7		NM_001258282.3	P1
	ENST00000566293.1	n.4336G>A		non_coding_transcript_exon_variant	1/1
LINGO2	ENST00000698405.1	n.813-694G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.283 AC: 42809 AN: 151504 Hom.: 6526 Cov.: 32

Gnomad AFR AF: 0.177

Gnomad AMI AF: 0.239

Gnomad AMR AF: 0.296

Gnomad ASJ AF: 0.358

Gnomad EAS AF: 0.332

Gnomad SAS AF: 0.422

Gnomad FIN AF: 0.223

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.334

Gnomad OTH AF: 0.330

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.282 AC: 42825 AN: 151620 Hom.: 6528 Cov.: 32 AF XY: 0.283 AC XY: 20931 AN XY: 74058

Gnomad4 AFR AF: 0.177

Gnomad4 AMR AF: 0.296

Gnomad4 ASJ AF: 0.358

Gnomad4 EAS AF: 0.332

Gnomad4 SAS AF: 0.421

Gnomad4 FIN AF: 0.223

Gnomad4 NFE AF: 0.333

Gnomad4 OTH AF: 0.327

Alfa AF: 0.302 Hom.: 1030

Bravo AF: 0.277

Asia WGS AF: 0.368 AC: 1281 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	2.0
Dann	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10968215; hg19: chr9-27940160;