Variant rs11633842 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001301186.2(LINGO1):c.-13+28091C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00866 in 152,340 control chromosomes in the GnomAD database, including 5 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 0.0087 ( 5 hom., cov: 33)

Exomes 𝑓: 0.083 ( 0 hom. )

Consequence

LINGO1
NM_001301186.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.562

Variant links:

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 links:

LINGO1-AS1 (HGNC:27368): (LINGO1 antisense RNA 1)

LINGO1-AS1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BA1

GnomAdExome4 highest population allele frequency = 0.0833 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Protein	UniProt
LINGO1	NM_001301186.2 link	c.-13+28091C>T	intron_variant	NP_001288115.1	Q96FE5-2
LINGO1	NM_001301187.2 link	c.-13+28091C>T	intron_variant	NP_001288116.1	Q96FE5-2
LINGO1	NM_001301189.2 link	c.-13+28091C>T	intron_variant	NP_001288118.1	Q96FE5-2

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	Protein	UniProt
LINGO1	ENST00000561030.5 link	c.-13+28091C>T	intron_variant		1	ENSP00000453853.1	Q96FE5-2
LINGO1-AS1	ENST00000558691.1 link	n.1478G>A	non_coding_transcript_exon_variant	3/3	1
LINGO1	ENST00000561686.5 link	c.-12-33098C>T	intron_variant		3	ENSP00000455605.1	H3BQ49

Frequencies

GnomAD3 genomes

AF:

0.00867

AC:

1319

AN:

152210

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00256

Gnomad AMI

AF:

0.0219

Gnomad AMR

AF:

0.00451

Gnomad ASJ

AF:

0.00548

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00665

Gnomad FIN

AF:

0.0151

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.0131

Gnomad OTH

AF:

0.00860

GnomAD4 exome

AF:

0.0833

AC:

AN:

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

show subpopulations

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.00

Gnomad4 OTH exome

AF:

0.500

GnomAD4 genome

AF:

0.00865

AC:

1318

AN:

152328

Hom.:

Cov.:

AF XY:

0.00888

AC XY:

661

AN XY:

74474

show subpopulations

Gnomad4 AFR

AF:

0.00255

Gnomad4 AMR

AF:

0.00451

Gnomad4 ASJ

AF:

0.00548

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00666

Gnomad4 FIN

AF:

0.0151

Gnomad4 NFE

AF:

0.0131

Gnomad4 OTH

AF:

0.00851

Alfa

AF:

0.00223

Hom.:

Bravo

AF:

0.00748

Asia WGS

AF:

0.00231

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.45

DANN

Benign

0.53

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over