rs7162113

Variant names:

• chr15-77622885-A-G
• rs7162113
• NM_032808.7:c.7-6985T>C

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_032808.7(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 NM_032808.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.145
• Publications: 5 publications found

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]

LINGO1 Gene-Disease associations (from GenCC):

• intellectual disability, autosomal recessive 64

  Inheritance: Unknown, AR Classification: LIMITED Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics

LOC105370906 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LINGO1	NM_032808.7	c.7-6985T>C		intron_variant	Intron 1 of 1	ENST00000355300.7	NP_116197.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINGO1	ENST00000355300.7	c.7-6985T>C		intron_variant	Intron 1 of 1	1	NM_032808.7	ENSP00000347451.6

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

African (AFR) AF: 0.945 AC: 39280 AN: 41554

American (AMR) AF: 0.836 AC: 12792 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.729 AC: 2531 AN: 3470

East Asian (EAS) AF: 0.866 AC: 4466 AN: 5160

South Asian (SAS) AF: 0.864 AC: 4166 AN: 4820

European-Finnish (FIN) AF: 0.832 AC: 8827 AN: 10606

Middle Eastern (MID) AF: 0.741 AC: 218 AN: 294

European-Non Finnish (NFE) AF: 0.777 AC: 52823 AN: 67996

Other (OTH) AF: 0.821 AC: 1730 AN: 2106

Alfa AF: 0.794 Hom.: 74147

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
PhyloP100		0.14
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs7162113; hg19: chr15-77915227;