rs9644872

Positions:

• chr9-27945760-G-A

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINGO2	NM_001258282.3	c.*3091C>T		3_prime_UTR_variant	7/7	ENST00000698399.1	NP_001245211.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINGO2	ENST00000698399.1	c.*3091C>T		3_prime_UTR_variant	7/7		NM_001258282.3	ENSP00000513694	P1
LINGO2	ENST00000698405.1	n.624-823C>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.154

Gnomad4 AMR AF: 0.488

Gnomad4 ASJ AF: 0.503

Gnomad4 EAS AF: 0.584

Gnomad4 SAS AF: 0.518

Gnomad4 FIN AF: 0.709

Gnomad4 NFE AF: 0.566

Gnomad4 OTH AF: 0.469

Alfa AF: 0.543 Hom.: 45896

Bravo AF: 0.427

Asia WGS AF: 0.505 AC: 1754 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

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