Variant rs3737336 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1

The NM_001378964.1(CDON):c.*140A>G variant causes a 3 prime UTR change. The variant allele was found at a frequency of 0.293 in 790,096 control chromosomes in the GnomAD database, including 35,027 homozygotes. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.25 ( 5477 hom., cov: 32)

Exomes 𝑓: 0.30 ( 29550 hom. )

Consequence

CDON
NM_001378964.1 3_prime_UTR

Scores

Clinical Significance

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

Conservation

PhyloP100: 4.78

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 -16 ACMG points.

BP6

Variant 11-125960802-T-C is Benign according to our data. Variant chr11-125960802-T-C is described in ClinVar as [Benign]. Clinvar id is 303488.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.309 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CDON	NM_001378964.1 link	c.*140A>G		3_prime_UTR_variant	20/20	ENST00000531738.6	NP_001365893.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CDON	ENST00000531738 link	c.*140A>G		3_prime_UTR_variant	20/20	1	NM_001378964.1	ENSP00000432901.2		Q4KMG0-2E9PN78

Frequencies

GnomAD3 genomes

AF:

0.255

AC:

38761

AN:

152022

Hom.:

5475

Cov.:

show subpopulations

Gnomad AFR

AF:

0.126

Gnomad AMI

AF:

0.302

Gnomad AMR

AF:

0.264

Gnomad ASJ

AF:

0.294

Gnomad EAS

AF:

0.284

Gnomad SAS

AF:

0.314

Gnomad FIN

AF:

0.318

Gnomad MID

AF:

0.250

Gnomad NFE

AF:

0.313

Gnomad OTH

AF:

0.251

GnomAD4 exome

AF:

0.302

AC:

192349

AN:

637956

Hom.:

29550

Cov.:

AF XY:

0.304

AC XY:

103436

AN XY:

340620

show subpopulations

Gnomad4 AFR exome

AF:

0.122

Gnomad4 AMR exome

AF:

0.278

Gnomad4 ASJ exome

AF:

0.297

Gnomad4 EAS exome

AF:

0.279

Gnomad4 SAS exome

AF:

0.316

Gnomad4 FIN exome

AF:

0.311

Gnomad4 NFE exome

AF:

0.312

Gnomad4 OTH exome

AF:

0.292

GnomAD4 genome

AF:

0.255

AC:

38780

AN:

152140

Hom.:

5477

Cov.:

AF XY:

0.257

AC XY:

19095

AN XY:

74356

show subpopulations

Gnomad4 AFR

AF:

0.126

Gnomad4 AMR

AF:

0.264

Gnomad4 ASJ

AF:

0.294

Gnomad4 EAS

AF:

0.284

Gnomad4 SAS

AF:

0.314

Gnomad4 FIN

AF:

0.318

Gnomad4 NFE

AF:

0.313

Gnomad4 OTH

AF:

0.250

Alfa

AF:

0.305

Hom.:

13753

Bravo

AF:

0.247

Asia WGS

AF:

0.271

AC:

944

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	Apr 12, 2019	- -

Holoprosencephaly 11

Benign:1

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. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Uncertain

-0.030

CADD

Benign

DANN

Benign

0.87

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