rs12367345

Variant names:

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001843.4(CNTN1):c.2711-17A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.144 in 1,492,160 control chromosomes in the GnomAD database, including 16,623 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.12 ( 1290 hom., cov: 32)

Exomes 𝑓: 0.15 ( 15333 hom. )

Consequence

CNTN1
NM_001843.4 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: -0.547

Publications

4 publications found

Variant links:

Genes affected

CNTN1 (HGNC:2171): (contactin 1) The protein encoded by this gene is a member of the immunoglobulin superfamily. It is a glycosylphosphatidylinositol (GPI)-anchored neuronal membrane protein that functions as a cell adhesion molecule. It may play a role in the formation of axon connections in the developing nervous system. Multiple alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2011]

CNTN1 Gene-Disease associations (from GenCC):

Compton-North congenital myopathy
Inheritance: AR Classification: STRONG, MODERATE, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics, Orphanet
schizophrenia
Inheritance: Unknown Classification: NO_KNOWN Submitted by: Labcorp Genetics (formerly Invitae)

CNTN1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.86).

BP6

Variant 12-41027840-A-G is Benign according to our data. Variant chr12-41027840-A-G is described in ClinVar as [Benign]. Clinvar id is 258196.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.154 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CNTN1	NM_001843.4 link	c.2711-17A>G		intron_variant	Intron 21 of 23	ENST00000551295.7	NP_001834.2	Q12860-1A0A024R104

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
CNTN1	ENST00000551295.7 link	c.2711-17A>G	intron_variant	Intron 21 of 23	1	NM_001843.4	ENSP00000447006.1	Q12860-1
CNTN1	ENST00000347616.5 link	c.2711-17A>G	intron_variant	Intron 20 of 22	1		ENSP00000325660.3	Q12860-1
CNTN1	ENST00000348761.2 link	c.2678-17A>G	intron_variant	Intron 19 of 21	1		ENSP00000261160.3	Q12860-2
CNTN1	ENST00000550305.1 link	n.670-17A>G	intron_variant	Intron 5 of 5	3

Frequencies

GnomAD3 genomes

AF:

0.120

AC:

18308

AN:

152016

Hom.:

1289

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0543

Gnomad AMI

AF:

0.110

Gnomad AMR

AF:

0.117

Gnomad ASJ

AF:

0.116

Gnomad EAS

AF:

0.0720

Gnomad SAS

AF:

0.0789

Gnomad FIN

AF:

0.195

Gnomad MID

AF:

0.0949

Gnomad NFE

AF:

0.157

Gnomad OTH

AF:

0.124

GnomAD2 exomes

AF:

0.128

AC:

32092

AN:

250542

AF XY:

0.129

show subpopulations

Gnomad AFR exome

AF:

0.0521

Gnomad AMR exome

AF:

0.110

Gnomad ASJ exome

AF:

0.112

Gnomad EAS exome

AF:

0.0750

Gnomad FIN exome

AF:

0.190

Gnomad NFE exome

AF:

0.156

Gnomad OTH exome

AF:

0.132

GnomAD4 exome

AF:

0.147

AC:

196985

AN:

1340026

Hom.:

15333

Cov.:

AF XY:

0.145

AC XY:

97783

AN XY:

673624

show subpopulations

African (AFR)

AF:

0.0518

AC:

1601

AN:

30926

American (AMR)

AF:

0.110

AC:

4880

AN:

44500

Ashkenazi Jewish (ASJ)

AF:

0.111

AC:

2819

AN:

25396

East Asian (EAS)

AF:

0.0571

AC:

2231

AN:

39060

South Asian (SAS)

AF:

0.0811

AC:

6791

AN:

83732

European-Finnish (FIN)

AF:

0.186

AC:

9900

AN:

53304

Middle Eastern (MID)

AF:

0.110

AC:

609

AN:

5520

European-Non Finnish (NFE)

AF:

0.160

AC:

160514

AN:

1001360

Other (OTH)

AF:

0.136

AC:

7640

AN:

56228

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.497

Heterozygous variant carriers

7644

15288

22931

30575

38219

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

5470

10940

16410

21880

27350

<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:

0.120

AC:

18308

AN:

152134

Hom.:

1290

Cov.:

AF XY:

0.120

AC XY:

8957

AN XY:

74360

show subpopulations

African (AFR)

AF:

0.0542

AC:

2252

AN:

41534

American (AMR)

AF:

0.117

AC:

1785

AN:

15268

Ashkenazi Jewish (ASJ)

AF:

0.116

AC:

401

AN:

3470

East Asian (EAS)

AF:

0.0717

AC:

371

AN:

5172

South Asian (SAS)

AF:

0.0790

AC:

381

AN:

4824

European-Finnish (FIN)

AF:

0.195

AC:

2067

AN:

10574

Middle Eastern (MID)

AF:

0.0952

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.157

AC:

10663

AN:

67974

Other (OTH)

AF:

0.123

AC:

260

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

807

1613

2420

3226

4033

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

214

428

642

856

1070

<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:

0.128

Hom.:

1262

Bravo

AF:

0.113

Asia WGS

AF:

0.0750

AC:

260

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:2

Feb 08, 2016

GeneDx

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

PreventionGenetics, part of Exact Sciences

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

not provided

Benign:1

Breakthrough Genomics, Breakthrough Genomics

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:not provided

- -

Compton-North congenital myopathy

Benign:1

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

0.021

(source)

DANN

Benign

0.64

PhyloP100

-0.55

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over