Variant rs11826465 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001378964.1(CDON):c.496+45C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.093 in 1,604,274 control chromosomes in the GnomAD database, including 7,336 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.10 ( 855 hom., cov: 32)

Exomes 𝑓: 0.092 ( 6481 hom. )

Consequence

CDON
NM_001378964.1 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.0740

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 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.97).

BP6

Variant 11-126019574-G-A is Benign according to our data. Variant chr11-126019574-G-A is described in ClinVar as [Benign]. Clinvar id is 260801.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.122 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CDON	NM_001378964.1 linkuse as main transcript	c.496+45C>T		intron_variant		ENST00000531738.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CDON	ENST00000531738.6 linkuse as main transcript	c.496+45C>T		intron_variant		1	NM_001378964.1	P1	Q4KMG0-2

Frequencies

GnomAD3 genomes

AF:

0.104

AC:

15813

AN:

151974

Hom.:

852

Cov.:

show subpopulations

Gnomad AFR

AF:

0.114

Gnomad AMI

AF:

0.0351

Gnomad AMR

AF:

0.126

Gnomad ASJ

AF:

0.105

Gnomad EAS

AF:

0.120

Gnomad SAS

AF:

0.123

Gnomad FIN

AF:

0.127

Gnomad MID

AF:

0.101

Gnomad NFE

AF:

0.0880

Gnomad OTH

AF:

0.100

GnomAD3 exomes

AF:

0.110

AC:

27488

AN:

251018

Hom.:

1612

AF XY:

0.108

AC XY:

14628

AN XY:

135662

show subpopulations

Gnomad AFR exome

AF:

0.118

Gnomad AMR exome

AF:

0.145

Gnomad ASJ exome

AF:

0.106

Gnomad EAS exome

AF:

0.136

Gnomad SAS exome

AF:

0.126

Gnomad FIN exome

AF:

0.128

Gnomad NFE exome

AF:

0.0862

Gnomad OTH exome

AF:

0.100

GnomAD4 exome

AF:

0.0918

AC:

133371

AN:

1452182

Hom.:

6481

Cov.:

AF XY:

0.0924

AC XY:

66807

AN XY:

723086

show subpopulations

Gnomad4 AFR exome

AF:

0.111

Gnomad4 AMR exome

AF:

0.141

Gnomad4 ASJ exome

AF:

0.107

Gnomad4 EAS exome

AF:

0.123

Gnomad4 SAS exome

AF:

0.120

Gnomad4 FIN exome

AF:

0.125

Gnomad4 NFE exome

AF:

0.0837

Gnomad4 OTH exome

AF:

0.0979

GnomAD4 genome

AF:

0.104

AC:

15845

AN:

152092

Hom.:

855

Cov.:

AF XY:

0.106

AC XY:

7887

AN XY:

74350

show subpopulations

Gnomad4 AFR

AF:

0.114

Gnomad4 AMR

AF:

0.126

Gnomad4 ASJ

AF:

0.105

Gnomad4 EAS

AF:

0.121

Gnomad4 SAS

AF:

0.123

Gnomad4 FIN

AF:

0.127

Gnomad4 NFE

AF:

0.0880

Gnomad4 OTH

AF:

0.104

Alfa

AF:

0.0958

Hom.:

144

Bravo

AF:

0.103

Asia WGS

AF:

0.163

AC:

565

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	clinical testing	GeneDx	Nov 10, 2018	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.97

CADD

Benign

5.9

DANN

Benign

0.64

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