chr11-125981160-A-G

Variant names:

Variant summary

Our verdict is Benign. The variant received -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_001378964.1(CDON):c.3165T>C(p.Asn1055Asn) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.272 in 1,613,738 control chromosomes in the GnomAD database, including 62,723 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.31 ( 8301 hom., cov: 32)

Exomes 𝑓: 0.27 ( 54422 hom. )

Consequence

CDON
NM_001378964.1 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:7

Conservation

PhyloP100: -1.91

Publications

20 publications found

Variant links:

Genes affected

CDON (HGNC:17104): (cell adhesion associated, oncogene regulated) This gene encodes a cell surface receptor that is a member of the immunoglobulin superfamily. The encoded protein contains three fibronectin type III domains and five immunoglobulin-like C2-type domains. This protein is a member of a cell-surface receptor complex that mediates cell-cell interactions between muscle precursor cells and positively regulates myogenesis. [provided by RefSeq, Aug 2011]

CDON Gene-Disease associations (from GenCC):

holoprosencephaly 11
Inheritance: AD Classification: DEFINITIVE, STRONG, MODERATE Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics, G2P, Illumina
pituitary stalk interruption syndrome
Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

CDON links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -21 ACMG points.

BP4

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

BP6

Variant 11-125981160-A-G is Benign according to our data. Variant chr11-125981160-A-G is described in ClinVar as Benign. ClinVar VariationId is 260792.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-1.91 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.453 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CDON	NM_001378964.1 link	c.3165T>C	p.Asn1055Asn	synonymous_variant	Exon 17 of 20	ENST00000531738.6	NP_001365893.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CDON	ENST00000531738.6 link	c.3165T>C	p.Asn1055Asn	synonymous_variant	Exon 17 of 20	1	NM_001378964.1	ENSP00000432901.2		Q4KMG0-2E9PN78

Frequencies

GnomAD3 genomes

AF:

0.315

AC:

47772

AN:

151872

Hom.:

8277

Cov.:

show subpopulations

Gnomad AFR

AF:

0.459

Gnomad AMI

AF:

0.455

Gnomad AMR

AF:

0.244

Gnomad ASJ

AF:

0.337

Gnomad EAS

AF:

0.0794

Gnomad SAS

AF:

0.210

Gnomad FIN

AF:

0.289

Gnomad MID

AF:

0.244

Gnomad NFE

AF:

0.271

Gnomad OTH

AF:

0.272

GnomAD2 exomes

AF:

0.256

AC:

64400

AN:

251404

AF XY:

0.252

show subpopulations

Gnomad AFR exome

AF:

0.467

Gnomad AMR exome

AF:

0.203

Gnomad ASJ exome

AF:

0.335

Gnomad EAS exome

AF:

0.0800

Gnomad FIN exome

AF:

0.302

Gnomad NFE exome

AF:

0.266

Gnomad OTH exome

AF:

0.251

GnomAD4 exome

AF:

0.267

AC:

390877

AN:

1461748

Hom.:

54422

Cov.:

AF XY:

0.265

AC XY:

192727

AN XY:

727180

show subpopulations

African (AFR)

AF:

0.466

AC:

15597

AN:

33478

American (AMR)

AF:

0.209

AC:

9353

AN:

44724

Ashkenazi Jewish (ASJ)

AF:

0.334

AC:

8740

AN:

26130

East Asian (EAS)

AF:

0.0795

AC:

3155

AN:

39700

South Asian (SAS)

AF:

0.222

AC:

19183

AN:

86258

European-Finnish (FIN)

AF:

0.299

AC:

15992

AN:

53416

Middle Eastern (MID)

AF:

0.230

AC:

1328

AN:

5766

European-Non Finnish (NFE)

AF:

0.271

AC:

301609

AN:

1111886

Other (OTH)

AF:

0.264

AC:

15920

AN:

60390

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.477

Heterozygous variant carriers

17201

34402

51602

68803

86004

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

10150

20300

30450

40600

50750

<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:

0.315

AC:

47849

AN:

151990

Hom.:

8301

Cov.:

AF XY:

0.310

AC XY:

23040

AN XY:

74286

show subpopulations

African (AFR)

AF:

0.459

AC:

19011

AN:

41422

American (AMR)

AF:

0.244

AC:

3736

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.337

AC:

1169

AN:

3468

East Asian (EAS)

AF:

0.0790

AC:

409

AN:

5176

South Asian (SAS)

AF:

0.211

AC:

1014

AN:

4814

European-Finnish (FIN)

AF:

0.289

AC:

3050

AN:

10560

Middle Eastern (MID)

AF:

0.252

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.271

AC:

18392

AN:

67950

Other (OTH)

AF:

0.275

AC:

580

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1610

3220

4831

6441

8051

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

448

896

1344

1792

2240

<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:

0.268

Hom.:

3387

Bravo

AF:

0.318

Asia WGS

AF:

0.206

AC:

717

AN:

3478

EpiCase

AF:

0.256

EpiControl

AF:

0.256

ClinVar

Significance: Benign

Submissions summary: Benign:7

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:3

Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen

Significance:Benign

Review Status:no assertion criteria provided

Collection Method:clinical testing

- -

Clinical Genetics, Academic Medical Center

Significance:Benign

Review Status:no assertion criteria provided

Collection Method:clinical testing

- -

PreventionGenetics, part of Exact Sciences

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

not provided

Benign:2

Breakthrough Genomics, Breakthrough Genomics

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:not provided

- -

Nov 10, 2018

GeneDx

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Holoprosencephaly 11

Benign:2

Jan 12, 2018

Illumina Laboratory Services, Illumina

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

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

0.022

(source)

DANN

Benign

0.31

PhyloP100

-1.9

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

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over