Variant chr11-126021267-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_001378964.1(CDON):c.330T>C(p.Pro110=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.042 in 1,614,038 control chromosomes in the GnomAD database, including 1,632 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.036 ( 131 hom., cov: 33)

Exomes 𝑓: 0.043 ( 1501 hom. )

Consequence

CDON
NM_001378964.1 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:5

Conservation

PhyloP100: -0.584

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 -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.56).

BP6

Variant 11-126021267-A-G is Benign according to our data. Variant chr11-126021267-A-G is described in ClinVar as [Benign]. Clinvar id is 95753.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-126021267-A-G is described in Lovd as [Likely_benign].

BP7

Synonymous conserved (PhyloP=-0.584 with no splicing effect.

BA1

GnomAdExome4 highest subpopulation (MID) allele frequency at 95% confidence interval = 0.0601 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.330T>C	p.Pro110=	synonymous_variant	3/20	ENST00000531738.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CDON	ENST00000531738.6 linkuse as main transcript	c.330T>C	p.Pro110=	synonymous_variant	3/20	1	NM_001378964.1	P1	Q4KMG0-2

Frequencies

GnomAD3 genomes

AF:

0.0357

AC:

5439

AN:

152224

Hom.:

131

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0230

Gnomad AMI

AF:

0.00987

Gnomad AMR

AF:

0.0458

Gnomad ASJ

AF:

0.0795

Gnomad EAS

AF:

0.00769

Gnomad SAS

AF:

0.0482

Gnomad FIN

AF:

0.0105

Gnomad MID

AF:

0.0854

Gnomad NFE

AF:

0.0436

Gnomad OTH

AF:

0.0574

GnomAD3 exomes

AF:

0.0373

AC:

9349

AN:

250814

Hom.:

251

AF XY:

0.0382

AC XY:

5183

AN XY:

135552

show subpopulations

Gnomad AFR exome

AF:

0.0218

Gnomad AMR exome

AF:

0.0323

Gnomad ASJ exome

AF:

0.0725

Gnomad EAS exome

AF:

0.00561

Gnomad SAS exome

AF:

0.0450

Gnomad FIN exome

AF:

0.0136

Gnomad NFE exome

AF:

0.0447

Gnomad OTH exome

AF:

0.0509

GnomAD4 exome

AF:

0.0426

AC:

62293

AN:

1461696

Hom.:

1501

Cov.:

AF XY:

0.0429

AC XY:

31191

AN XY:

727134

show subpopulations

Gnomad4 AFR exome

AF:

0.0218

Gnomad4 AMR exome

AF:

0.0334

Gnomad4 ASJ exome

AF:

0.0742

Gnomad4 EAS exome

AF:

0.00612

Gnomad4 SAS exome

AF:

0.0455

Gnomad4 FIN exome

AF:

0.0150

Gnomad4 NFE exome

AF:

0.0450

Gnomad4 OTH exome

AF:

0.0453

GnomAD4 genome

AF:

0.0357

AC:

5435

AN:

152342

Hom.:

131

Cov.:

AF XY:

0.0348

AC XY:

2594

AN XY:

74504

show subpopulations

Gnomad4 AFR

AF:

0.0229

Gnomad4 AMR

AF:

0.0457

Gnomad4 ASJ

AF:

0.0795

Gnomad4 EAS

AF:

0.00771

Gnomad4 SAS

AF:

0.0485

Gnomad4 FIN

AF:

0.0105

Gnomad4 NFE

AF:

0.0436

Gnomad4 OTH

AF:

0.0568

Alfa

AF:

0.0419

Hom.:

Bravo

AF:

0.0380

Asia WGS

AF:

0.0250

AC:

AN:

3478

EpiCase

AF:

0.0473

EpiControl

AF:

0.0499

ClinVar

Significance: Benign

Submissions summary: Benign:5

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:2

Benign, criteria provided, single submitter	clinical testing	PreventionGenetics, part of Exact Sciences	-	- -
Benign, criteria provided, single submitter	clinical testing	Eurofins Ntd Llc (ga)	Aug 07, 2013	- -

Holoprosencephaly 11

Benign:2

Benign, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Jan 12, 2018	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. -
Benign, criteria provided, single submitter	clinical testing	Invitae	Jan 29, 2024	- -

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Apr 07, 2020

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.56

CADD

Benign

0.81

DANN

Benign

0.46

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