dbSNP rs1521179: LINGO4:c.*12C>T (chr1-151800911-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001004432.4(LINGO4):c.*12C>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 0.0366 in 1,585,980 control chromosomes in the GnomAD database, including 7,100 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 0.058 ( 819 hom., cov: 33)

Exomes 𝑓: 0.034 ( 6281 hom. )

Consequence

LINGO4
NM_001004432.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.827

Publications

6 publications found

Variant links:

Genes affected

LINGO4 (HGNC:31814): (leucine rich repeat and Ig domain containing 4) 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]

LINGO4 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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 = 0.349 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINGO4	NM_001004432.4 link	c.*12C>T		3_prime_UTR_variant	Exon 2 of 2	ENST00000368820.4	NP_001004432.1	Q6UY18

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINGO4	ENST00000368820.4 link	c.*12C>T		3_prime_UTR_variant	Exon 2 of 2	1	NM_001004432.4	ENSP00000357810.4		Q6UY18

Frequencies

GnomAD3 genomes

AF:

0.0580

AC:

8824

AN:

152098

Hom.:

821

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0889

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.116

Gnomad ASJ

AF:

0.00259

Gnomad EAS

AF:

0.363

Gnomad SAS

AF:

0.241

Gnomad FIN

AF:

0.000282

Gnomad MID

AF:

0.0475

Gnomad NFE

AF:

0.00285

Gnomad OTH

AF:

0.0573

GnomAD2 exomes

AF:

0.100

AC:

23141

AN:

231370

AF XY:

0.0959

show subpopulations

Gnomad AFR exome

AF:

0.0906

Gnomad AMR exome

AF:

0.247

Gnomad ASJ exome

AF:

0.00159

Gnomad EAS exome

AF:

0.391

Gnomad FIN exome

AF:

0.000490

Gnomad NFE exome

AF:

0.00274

Gnomad OTH exome

AF:

0.0586

GnomAD4 exome

AF:

0.0343

AC:

49229

AN:

1433764

Hom.:

6281

Cov.:

AF XY:

0.0383

AC XY:

27218

AN XY:

709742

show subpopulations

African (AFR)

AF:

0.0938

AC:

3064

AN:

32658

American (AMR)

AF:

0.232

AC:

9760

AN:

42000

Ashkenazi Jewish (ASJ)

AF:

0.00193

AC:

AN:

24386

East Asian (EAS)

AF:

0.334

AC:

13130

AN:

39334

South Asian (SAS)

AF:

0.222

AC:

18206

AN:

82092

European-Finnish (FIN)

AF:

0.000383

AC:

AN:

52280

Middle Eastern (MID)

AF:

0.0300

AC:

169

AN:

5632

European-Non Finnish (NFE)

AF:

0.00194

AC:

2132

AN:

1096346

Other (OTH)

AF:

0.0458

AC:

2701

AN:

59036

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

2164

4328

6492

8656

10820

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

702

1404

2106

2808

3510

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0580

AC:

8821

AN:

152216

Hom.:

819

Cov.:

AF XY:

0.0638

AC XY:

4751

AN XY:

74432

show subpopulations

African (AFR)

AF:

0.0890

AC:

3695

AN:

41532

American (AMR)

AF:

0.116

AC:

1767

AN:

15298

Ashkenazi Jewish (ASJ)

AF:

0.00259

AC:

AN:

3472

East Asian (EAS)

AF:

0.363

AC:

1862

AN:

5128

South Asian (SAS)

AF:

0.240

AC:

1158

AN:

4826

European-Finnish (FIN)

AF:

0.000282

AC:

AN:

10626

Middle Eastern (MID)

AF:

0.0476

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00285

AC:

194

AN:

68012

Other (OTH)

AF:

0.0562

AC:

119

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

364

728

1093

1457

1821

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

116

232

348

464

580

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0227

Hom.:

109

Bravo

AF:

0.0706

Asia WGS

AF:

0.227

AC:

789

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

2.7

(source)

DANN

Benign

0.80

PhyloP100

-0.83

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over