rs7119527

Variant names:

• chr11-126017416-C-T
• rs7119527
• NM_001378964.1:c.641-41G>A

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.641-41G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0937 in 1,583,714 control chromosomes in the GnomAD database, including 7,264 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.10 (862 hom., cov: 32)
  • Exomes 𝑓: 0.093 (6402 hom.)
• Consequence: CDON NM_001378964.1 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:3
• Conservation: PhyloP100: 0.0240

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=-0.83).
• BP6: Variant 11-126017416-C-T is Benign according to our data. Variant chr11-126017416-C-T is described in ClinVar as [Benign]. Clinvar id is 260804.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 rank	MANE	Protein	UniProt
CDON	NM_001378964.1	c.641-41G>A		intron_variant	Intron 5 of 19	ENST00000531738.6	NP_001365893.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CDON	ENST00000531738.6	c.641-41G>A		intron_variant	Intron 5 of 19	1	NM_001378964.1	ENSP00000432901.2

Frequencies

GnomAD3 genomes AF: 0.104 AC: 15805 AN: 152104 Hom.: 859 Cov.: 32

Gnomad AFR AF: 0.114

Gnomad AMI AF: 0.0351

Gnomad AMR AF: 0.126

Gnomad ASJ AF: 0.0983

Gnomad EAS AF: 0.121

Gnomad SAS AF: 0.122

Gnomad FIN AF: 0.127

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.0879

Gnomad OTH AF: 0.101

GnomAD3 exomes AF: 0.110 AC: 26672 AN: 242854 Hom.: 1538 AF XY: 0.108 AC XY: 14131 AN XY: 131090

Gnomad AFR exome AF: 0.120

Gnomad AMR exome AF: 0.146

Gnomad ASJ exome AF: 0.103

Gnomad EAS exome AF: 0.137

Gnomad SAS exome AF: 0.122

Gnomad FIN exome AF: 0.129

Gnomad NFE exome AF: 0.0867

Gnomad OTH exome AF: 0.0999

GnomAD4 exome AF: 0.0926 AC: 132585 AN: 1431492 Hom.: 6402 Cov.: 26 AF XY: 0.0928 AC XY: 66238 AN XY: 713446

Gnomad4 AFR exome AF: 0.113

Gnomad4 AMR exome AF: 0.141

Gnomad4 ASJ exome AF: 0.103

Gnomad4 EAS exome AF: 0.122

Gnomad4 SAS exome AF: 0.117

Gnomad4 FIN exome AF: 0.125

Gnomad4 NFE exome AF: 0.0850

Gnomad4 OTH exome AF: 0.0980

GnomAD4 genome AF: 0.104 AC: 15837 AN: 152222 Hom.: 862 Cov.: 32 AF XY: 0.106 AC XY: 7888 AN XY: 74428

Gnomad4 AFR AF: 0.114

Gnomad4 AMR AF: 0.126

Gnomad4 ASJ AF: 0.0983

Gnomad4 EAS AF: 0.122

Gnomad4 SAS AF: 0.122

Gnomad4 FIN AF: 0.127

Gnomad4 NFE AF: 0.0879

Gnomad4 OTH AF: 0.104

Alfa AF: 0.0914 Hom.: 672

Bravo AF: 0.103

Asia WGS AF: 0.162 AC: 561 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

-

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Nov 10, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

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	3.0
DANN	Benign	0.36

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: rs7119527; hg19: chr11-125887311;