rs7162113

Positions:

• chr15-77622885-A-G
• chr15-77622885-A-T

Variant summary

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

The ENST00000355300.7(LINGO1):​c.7-6985T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.838 in 152,212 control chromosomes in the GnomAD database, including 53,791 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 0.84 (53791 hom., cov: 33)
• Consequence: LINGO1 ENST00000355300.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.145

Genes affected

LINGO1 (HGNC:21205): (leucine rich repeat and Ig domain containing 1) Predicted to enable epidermal growth factor receptor binding activity. Predicted to act upstream of or within generation of neurons and protein kinase B signaling. Predicted to be located in plasma membrane. Predicted to be active in extracellular matrix and extracellular space. Implicated in autosomal recessive non-syndromic intellectual disability and glaucoma. [provided by Alliance of Genome Resources, Apr 2022]

LOC105370906 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.937 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINGO1	NM_032808.7	c.7-6985T>C		intron_variant		ENST00000355300.7	NP_116197.4
LOC105370906	XR_001751806.2	n.689-7400A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINGO1	ENST00000355300.7	c.7-6985T>C		intron_variant		1	NM_032808.7	ENSP00000347451	A1

Frequencies

GnomAD3 genomes AF: 0.837 AC: 127361 AN: 152094 Hom.: 53730 Cov.: 33

Gnomad AFR AF: 0.945

Gnomad AMI AF: 0.713

Gnomad AMR AF: 0.836

Gnomad ASJ AF: 0.729

Gnomad EAS AF: 0.866

Gnomad SAS AF: 0.865

Gnomad FIN AF: 0.832

Gnomad MID AF: 0.741

Gnomad NFE AF: 0.777

Gnomad OTH AF: 0.824

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

GnomAD4 genome AF: 0.838 AC: 127482 AN: 152212 Hom.: 53791 Cov.: 33 AF XY: 0.842 AC XY: 62693 AN XY: 74424

Gnomad4 AFR AF: 0.945

Gnomad4 AMR AF: 0.836

Gnomad4 ASJ AF: 0.729

Gnomad4 EAS AF: 0.866

Gnomad4 SAS AF: 0.864

Gnomad4 FIN AF: 0.832

Gnomad4 NFE AF: 0.777

Gnomad4 OTH AF: 0.821

Alfa AF: 0.788 Hom.: 56292

Bravo AF: 0.841

Asia WGS AF: 0.832 AC: 2891 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.3
DANN	Benign	0.64

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: rs7162113; hg19: chr15-77915227;