Variant rs9787172 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BA1

The NM_005076.5(CNTN2):c.297C>T(p.Asn99Asn) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0351 in 1,548,416 control chromosomes in the GnomAD database, including 1,704 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.052 ( 328 hom., cov: 32)

Exomes 𝑓: 0.033 ( 1376 hom. )

Consequence

CNTN2
NM_005076.5 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: 1.06

Variant links:

Genes affected

CNTN2 (HGNC:2172): (contactin 2) This gene encodes a member of the contactin family of proteins, part of the immunoglobulin superfamily of cell adhesion molecules. The encoded glycosylphosphatidylinositol (GPI)-anchored neuronal membrane protein plays a role in the proliferation, migration, and axon guidance of neurons of the developing cerebellum. A mutation in this gene may be associated with adult myoclonic epilepsy. [provided by RefSeq, Sep 2016]

CNTN2 links:

CNTN2 (HGNC:):

CNTN2 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -19 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.37).

BP6

Variant 1-205058262-C-T is Benign according to our data. Variant chr1-205058262-C-T is described in ClinVar as [Benign]. Clinvar id is 474482.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=1.06 with no splicing effect.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.116 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CNTN2	NM_005076.5 linkuse as main transcript	c.297C>T	p.Asn99Asn	synonymous_variant	4/23	ENST00000331830.7	NP_005067.1	Q02246A1ML24A1L3A3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CNTN2	ENST00000331830.7 linkuse as main transcript	c.297C>T	p.Asn99Asn	synonymous_variant	4/23	1	NM_005076.5	ENSP00000330633.4		Q02246

Frequencies

GnomAD3 genomes

AF:

0.0523

AC:

7959

AN:

152070

Hom.:

322

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0927

Gnomad AMI

AF:

0.00110

Gnomad AMR

AF:

0.0340

Gnomad ASJ

AF:

0.0671

Gnomad EAS

AF:

0.0210

Gnomad SAS

AF:

0.124

Gnomad FIN

AF:

0.0852

Gnomad MID

AF:

0.0573

Gnomad NFE

AF:

0.0243

Gnomad OTH

AF:

0.0440

GnomAD3 exomes

AF:

0.0468

AC:

9240

AN:

197604

Hom.:

358

AF XY:

0.0489

AC XY:

5116

AN XY:

104522

show subpopulations

Gnomad AFR exome

AF:

0.0960

Gnomad AMR exome

AF:

0.0220

Gnomad ASJ exome

AF:

0.0662

Gnomad EAS exome

AF:

0.0158

Gnomad SAS exome

AF:

0.129

Gnomad FIN exome

AF:

0.0832

Gnomad NFE exome

AF:

0.0270

Gnomad OTH exome

AF:

0.0406

GnomAD4 exome

AF:

0.0332

AC:

46419

AN:

1396228

Hom.:

1376

Cov.:

AF XY:

0.0355

AC XY:

24375

AN XY:

687328

show subpopulations

Gnomad4 AFR exome

AF:

0.0919

Gnomad4 AMR exome

AF:

0.0237

Gnomad4 ASJ exome

AF:

0.0648

Gnomad4 EAS exome

AF:

0.0227

Gnomad4 SAS exome

AF:

0.120

Gnomad4 FIN exome

AF:

0.0806

Gnomad4 NFE exome

AF:

0.0230

Gnomad4 OTH exome

AF:

0.0392

GnomAD4 genome

AF:

0.0524

AC:

7981

AN:

152188

Hom.:

328

Cov.:

AF XY:

0.0554

AC XY:

4125

AN XY:

74420

show subpopulations

Gnomad4 AFR

AF:

0.0926

Gnomad4 AMR

AF:

0.0339

Gnomad4 ASJ

AF:

0.0671

Gnomad4 EAS

AF:

0.0215

Gnomad4 SAS

AF:

0.124

Gnomad4 FIN

AF:

0.0852

Gnomad4 NFE

AF:

0.0243

Gnomad4 OTH

AF:

0.0482

Alfa

AF:

0.0415

Hom.:

Bravo

AF:

0.0477

Asia WGS

AF:

0.0900

AC:

312

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Oct 15, 2018	- -

Epilepsy, familial adult myoclonic, 5

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Feb 01, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.37

CADD

Benign

9.5

DANN

Benign

0.78

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

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over