Genetic Variant CDON:c.2545-42A>G (chr11-125994431-T-C) – ACMG Classification: Benign (-20 pts)

Variant summary

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

The NM_001378964.1(CDON):c.2545-42A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.307 in 1,065,142 control chromosomes in the GnomAD database, including 50,092 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.30 ( 6946 hom., cov: 32)

Exomes 𝑓: 0.31 ( 43146 hom. )

Consequence

CDON
NM_001378964.1 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: 0.0560

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=-0.83).

BP6

Variant 11-125994431-T-C is Benign according to our data. Variant chr11-125994431-T-C is described in ClinVar as [Benign]. Clinvar id is 260788.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.324 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CDON	NM_001378964.1 link	c.2545-42A>G		intron_variant	Intron 13 of 19	ENST00000531738.6	NP_001365893.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CDON	ENST00000531738.6 link	c.2545-42A>G		intron_variant	Intron 13 of 19	1	NM_001378964.1	ENSP00000432901.2		Q4KMG0-2E9PN78

Frequencies

GnomAD3 genomes

AF:

0.300

AC:

45655

AN:

151976

Hom.:

6931

Cov.:

show subpopulations

Gnomad AFR

AF:

0.292

Gnomad AMI

AF:

0.222

Gnomad AMR

AF:

0.296

Gnomad ASJ

AF:

0.351

Gnomad EAS

AF:

0.288

Gnomad SAS

AF:

0.337

Gnomad FIN

AF:

0.369

Gnomad MID

AF:

0.313

Gnomad NFE

AF:

0.293

Gnomad OTH

AF:

0.283

GnomAD3 exomes

AF:

0.313

AC:

72317

AN:

230896

Hom.:

11163

AF XY:

0.316

AC XY:

39382

AN XY:

124696

show subpopulations

Gnomad AFR exome

AF:

0.299

Gnomad AMR exome

AF:

0.302

Gnomad ASJ exome

AF:

0.352

Gnomad EAS exome

AF:

0.281

Gnomad SAS exome

AF:

0.345

Gnomad FIN exome

AF:

0.369

Gnomad NFE exome

AF:

0.300

Gnomad OTH exome

AF:

0.326

GnomAD4 exome

AF:

0.308

AC:

280810

AN:

913048

Hom.:

43146

Cov.:

AF XY:

0.309

AC XY:

147218

AN XY:

477106

show subpopulations

Gnomad4 AFR exome

AF:

0.300

Gnomad4 AMR exome

AF:

0.300

Gnomad4 ASJ exome

AF:

0.352

Gnomad4 EAS exome

AF:

0.276

Gnomad4 SAS exome

AF:

0.343

Gnomad4 FIN exome

AF:

0.357

Gnomad4 NFE exome

AF:

0.300

Gnomad4 OTH exome

AF:

0.315

GnomAD4 genome

AF:

0.301

AC:

45713

AN:

152094

Hom.:

6946

Cov.:

AF XY:

0.303

AC XY:

22544

AN XY:

74332

show subpopulations

Gnomad4 AFR

AF:

0.293

Gnomad4 AMR

AF:

0.296

Gnomad4 ASJ

AF:

0.351

Gnomad4 EAS

AF:

0.288

Gnomad4 SAS

AF:

0.337

Gnomad4 FIN

AF:

0.369

Gnomad4 NFE

AF:

0.293

Gnomad4 OTH

AF:

0.282

Alfa

AF:

0.301

Hom.:

3615

Bravo

AF:

0.297

Asia WGS

AF:

0.304

AC:

1057

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

Nov 10, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

not specified

Benign:1

PreventionGenetics, part of Exact Sciences

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

-0.83

CADD

Benign

1.6

DANN

Benign

0.66

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