rs75029148

chr11-126019569-A-G

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_001378964.1(CDON):c.496+50T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0882 in 1,600,460 control chromosomes in the GnomAD database, including 6,747 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.080 (593 hom., cov: 32)
  • Exomes 𝑓: 0.089 (6154 hom.)
• Consequence: CDON NM_001378964.1 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -0.167

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]

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BP6: Variant 11-126019569-A-G is Benign according to our data. Variant chr11-126019569-A-G is described in ClinVar as [Benign]. Clinvar id is 260802.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.115 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CDON	NM_001378964.1	c.496+50T>C		intron_variant		ENST00000531738.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CDON	ENST00000531738.6	c.496+50T>C		intron_variant		1	NM_001378964.1	P1

Frequencies

GnomAD3 genomes AF: 0.0797 AC: 12110 AN: 152036 Hom.: 592 Cov.: 32

Gnomad AFR AF: 0.0291

Gnomad AMI AF: 0.0351

Gnomad AMR AF: 0.118

Gnomad ASJ AF: 0.105

Gnomad EAS AF: 0.119

Gnomad SAS AF: 0.123

Gnomad FIN AF: 0.127

Gnomad MID AF: 0.0955

Gnomad NFE AF: 0.0875

Gnomad OTH AF: 0.0856

GnomAD3 exomes AF: 0.103 AC: 25756 AN: 250910 Hom.: 1462 AF XY: 0.103 AC XY: 13953 AN XY: 135606

Gnomad AFR exome AF: 0.0268

Gnomad AMR exome AF: 0.140

Gnomad ASJ exome AF: 0.107

Gnomad EAS exome AF: 0.136

Gnomad SAS exome AF: 0.125

Gnomad FIN exome AF: 0.127

Gnomad NFE exome AF: 0.0858

Gnomad OTH exome AF: 0.0975

GnomAD4 exome AF: 0.0891 AC: 129109 AN: 1448306 Hom.: 6154 Cov.: 28 AF XY: 0.0901 AC XY: 64970 AN XY: 721414

Gnomad4 AFR exome AF: 0.0251

Gnomad4 AMR exome AF: 0.136

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: 0.0833

Gnomad4 OTH exome AF: 0.0927

GnomAD4 genome AF: 0.0797 AC: 12124 AN: 152154 Hom.: 593 Cov.: 32 AF XY: 0.0823 AC XY: 6122 AN XY: 74366

Gnomad4 AFR AF: 0.0290

Gnomad4 AMR AF: 0.118

Gnomad4 ASJ AF: 0.105

Gnomad4 EAS AF: 0.120

Gnomad4 SAS AF: 0.123

Gnomad4 FIN AF: 0.127

Gnomad4 NFE AF: 0.0875

Gnomad4 OTH AF: 0.0894

Alfa AF: 0.0845 Hom.: 118

Bravo AF: 0.0747

Asia WGS AF: 0.158 AC: 548 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not specified Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

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- -

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 10, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	6.6
Dann	Benign	0.59

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

Other links and lift over

dbSNP: rs75029148; hg19: chr11-125889464; COSMIC: COSV54996046; COSMIC: COSV54996046;