rs10511830

chr9-28644925-A-G

Variant summary

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

The NM_001258282.3(LINGO2):c.-314+25275T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.09 in 152,080 control chromosomes in the GnomAD database, including 876 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 0.090 (876 hom., cov: 32)
• Consequence: LINGO2 NM_001258282.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.163

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]

LOC105376003 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.217 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINGO2	NM_001258282.3	c.-314+25275T>C		intron_variant		ENST00000698399.1
LOC105376003	XR_929533.4	n.294-11976A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINGO2	ENST00000698399.1	c.-314+25275T>C		intron_variant			NM_001258282.3	P1

Frequencies

GnomAD3 genomes AF: 0.0899 AC: 13657 AN: 151962 Hom.: 868 Cov.: 32

Gnomad AFR AF: 0.0988

Gnomad AMI AF: 0.0702

Gnomad AMR AF: 0.222

Gnomad ASJ AF: 0.0516

Gnomad EAS AF: 0.0744

Gnomad SAS AF: 0.0979

Gnomad FIN AF: 0.0858

Gnomad MID AF: 0.0478

Gnomad NFE AF: 0.0588

Gnomad OTH AF: 0.0808

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

GnomAD4 genome AF: 0.0900 AC: 13684 AN: 152080 Hom.: 876 Cov.: 32 AF XY: 0.0935 AC XY: 6950 AN XY: 74346

Gnomad4 AFR AF: 0.0989

Gnomad4 AMR AF: 0.223

Gnomad4 ASJ AF: 0.0516

Gnomad4 EAS AF: 0.0745

Gnomad4 SAS AF: 0.0978

Gnomad4 FIN AF: 0.0858

Gnomad4 NFE AF: 0.0587

Gnomad4 OTH AF: 0.0799

Alfa AF: 0.0700 Hom.: 224

Bravo AF: 0.103

Asia WGS AF: 0.130 AC: 450 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	1.4
Dann	Benign	0.51

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

Publications

LitVar

Other links and lift over

dbSNP: rs10511830; hg19: chr9-28644923;