rs1939890

Variant names:

Your query was ambiguous. Multiple possible variants found:

Variant summary

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

The NM_001378964.1(CDON):c.76+21G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.186 in 1,515,102 control chromosomes in the GnomAD database, including 26,932 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.17 ( 2384 hom., cov: 32)

Exomes 𝑓: 0.19 ( 24548 hom. )

Consequence

CDON
NM_001378964.1 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: -1.27

Publications

10 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: Ambry Genetics, Illumina, Labcorp Genetics (formerly Invitae), G2P
pituitary stalk interruption syndrome
Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

CDON links:

Genome browser will be placed here

new If you want to explore the variant's impact on the transcript NM_001378964.1, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

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=-0.91).

BP6

Variant 11-126023380-C-T is Benign according to our data. Variant chr11-126023380-C-T is described in ClinVar as Benign. ClinVar VariationId is 260805.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.195 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001378964.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
CDON	NM_001378964.1	MANE Select	c.76+21G>A	intron	N/A	NP_001365893.1	Q4KMG0-2
CDON	NM_001243597.3		c.76+21G>A	intron	N/A	NP_001230526.1
CDON	NM_001441161.1		c.76+21G>A	intron	N/A	NP_001428090.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
CDON	ENST00000531738.6	TSL:1 MANE Select	c.76+21G>A	intron	N/A	ENSP00000432901.2	Q4KMG0-2
CDON	ENST00000392693.7	TSL:1	c.76+21G>A	intron	N/A	ENSP00000376458.3	Q4KMG0-1
CDON	ENST00000263577.11	TSL:1	c.76+21G>A	intron	N/A	ENSP00000263577.7	Q4KMG0-2

Frequencies

GnomAD3 genomes

AF:

0.170

AC:

25891

AN:

151860

Hom.:

2384

Cov.:

show subpopulations

Gnomad AFR

AF:

0.116

Gnomad AMI

AF:

0.195

Gnomad AMR

AF:

0.178

Gnomad ASJ

AF:

0.194

Gnomad EAS

AF:

0.159

Gnomad SAS

AF:

0.205

Gnomad FIN

AF:

0.199

Gnomad MID

AF:

0.153

Gnomad NFE

AF:

0.195

Gnomad OTH

AF:

0.156

GnomAD2 exomes

AF:

0.183

AC:

46041

AN:

251086

AF XY:

0.184

show subpopulations

Gnomad AFR exome

AF:

0.116

Gnomad AMR exome

AF:

0.179

Gnomad ASJ exome

AF:

0.198

Gnomad EAS exome

AF:

0.174

Gnomad FIN exome

AF:

0.200

Gnomad NFE exome

AF:

0.185

Gnomad OTH exome

AF:

0.181

GnomAD4 exome

AF:

0.187

AC:

255288

AN:

1363124

Hom.:

24548

Cov.:

AF XY:

0.188

AC XY:

128550

AN XY:

684154

show subpopulations

African (AFR)

AF:

0.111

AC:

3495

AN:

31462

American (AMR)

AF:

0.177

AC:

7903

AN:

44630

Ashkenazi Jewish (ASJ)

AF:

0.196

AC:

5015

AN:

25540

East Asian (EAS)

AF:

0.158

AC:

6219

AN:

39248

South Asian (SAS)

AF:

0.203

AC:

17103

AN:

84388

European-Finnish (FIN)

AF:

0.199

AC:

10642

AN:

53348

Middle Eastern (MID)

AF:

0.125

AC:

696

AN:

5554

European-Non Finnish (NFE)

AF:

0.189

AC:

193432

AN:

1021874

Other (OTH)

AF:

0.189

AC:

10783

AN:

57080

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.492

Heterozygous variant carriers

9593

19187

28780

38374

47967

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

6564

13128

19692

26256

32820

<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:

0.171

AC:

25918

AN:

151978

Hom.:

2384

Cov.:

AF XY:

0.171

AC XY:

12690

AN XY:

74256

show subpopulations

African (AFR)

AF:

0.116

AC:

4824

AN:

41474

American (AMR)

AF:

0.178

AC:

2716

AN:

15244

Ashkenazi Jewish (ASJ)

AF:

0.194

AC:

674

AN:

3472

East Asian (EAS)

AF:

0.159

AC:

821

AN:

5148

South Asian (SAS)

AF:

0.206

AC:

988

AN:

4798

European-Finnish (FIN)

AF:

0.199

AC:

2102

AN:

10550

Middle Eastern (MID)

AF:

0.154

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.195

AC:

13233

AN:

67978

Other (OTH)

AF:

0.160

AC:

338

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1092

2185

3277

4370

5462

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

282

564

846

1128

1410

<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:

0.178

Hom.:

4760

Bravo

AF:

0.163

Asia WGS

AF:

0.229

AC:

796

AN:

3478

ClinVar

ClinVar submissions

Significance:Benign

Revision:criteria provided, multiple submitters, no conflicts

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (2)

not specified (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.35

(source)

DANN

Benign

0.63

PhyloP100

-1.3

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over