Variant rs3824922 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.2996-48G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0497 in 1,570,440 control chromosomes in the GnomAD database, including 2,675 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.046 ( 262 hom., cov: 32)

Exomes 𝑓: 0.050 ( 2413 hom. )

Consequence

CDON
NM_001378964.1 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 1.19

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=-0.59).

BP6

Variant 11-125981377-C-A is Benign according to our data. Variant chr11-125981377-C-A is described in ClinVar as [Benign]. Clinvar id is 260790.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.121 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.2996-48G>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.2996-48G>T		intron_variant		1	NM_001378964.1	P1	Q4KMG0-2

Frequencies

GnomAD3 genomes

AF:

0.0458

AC:

6870

AN:

149968

Hom.:

263

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0170

Gnomad AMI

AF:

0.0246

Gnomad AMR

AF:

0.126

Gnomad ASJ

AF:

0.0107

Gnomad EAS

AF:

0.103

Gnomad SAS

AF:

0.0798

Gnomad FIN

AF:

0.0302

Gnomad MID

AF:

0.0446

Gnomad NFE

AF:

0.0429

Gnomad OTH

AF:

0.0496

GnomAD3 exomes

AF:

0.0637

AC:

15087

AN:

236944

Hom.:

726

AF XY:

0.0606

AC XY:

7812

AN XY:

128870

show subpopulations

Gnomad AFR exome

AF:

0.0154

Gnomad AMR exome

AF:

0.143

Gnomad ASJ exome

AF:

0.00958

Gnomad EAS exome

AF:

0.110

Gnomad SAS exome

AF:

0.0757

Gnomad FIN exome

AF:

0.0338

Gnomad NFE exome

AF:

0.0439

Gnomad OTH exome

AF:

0.0506

GnomAD4 exome

AF:

0.0502

AC:

71245

AN:

1420354

Hom.:

2413

Cov.:

AF XY:

0.0504

AC XY:

35679

AN XY:

708100

show subpopulations

Gnomad4 AFR exome

AF:

0.0135

Gnomad4 AMR exome

AF:

0.140

Gnomad4 ASJ exome

AF:

0.00858

Gnomad4 EAS exome

AF:

0.109

Gnomad4 SAS exome

AF:

0.0727

Gnomad4 FIN exome

AF:

0.0334

Gnomad4 NFE exome

AF:

0.0453

Gnomad4 OTH exome

AF:

0.0518

GnomAD4 genome

AF:

0.0457

AC:

6865

AN:

150086

Hom.:

262

Cov.:

AF XY:

0.0482

AC XY:

3529

AN XY:

73246

show subpopulations

Gnomad4 AFR

AF:

0.0169

Gnomad4 AMR

AF:

0.126

Gnomad4 ASJ

AF:

0.0107

Gnomad4 EAS

AF:

0.103

Gnomad4 SAS

AF:

0.0788

Gnomad4 FIN

AF:

0.0302

Gnomad4 NFE

AF:

0.0430

Gnomad4 OTH

AF:

0.0515

Alfa

AF:

0.0130

Hom.:

Bravo

AF:

0.0487

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

- -

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Aug 06, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.59

CADD

Benign

2.8

DANN

Benign

0.44

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