rs472926

Positions:

• chr11-126035363-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001378964.1(CDON):​c.-61-11826G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.877 in 152,232 control chromosomes in the GnomAD database, including 58,708 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.88 (58708 hom., cov: 32)
• Consequence: CDON NM_001378964.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.67

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.962 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CDON	NM_001378964.1	c.-61-11826G>A		intron_variant		ENST00000531738.6	NP_001365893.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CDON	ENST00000531738.6	c.-61-11826G>A		intron_variant		1	NM_001378964.1	ENSP00000432901	P1

Frequencies

GnomAD3 genomes AF: 0.876 AC: 133309 AN: 152114 Hom.: 58643 Cov.: 32

Gnomad AFR AF: 0.970

Gnomad AMI AF: 0.888

Gnomad AMR AF: 0.828

Gnomad ASJ AF: 0.876

Gnomad EAS AF: 0.838

Gnomad SAS AF: 0.815

Gnomad FIN AF: 0.835

Gnomad MID AF: 0.896

Gnomad NFE AF: 0.844

Gnomad OTH AF: 0.854

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.877 AC: 133433 AN: 152232 Hom.: 58708 Cov.: 32 AF XY: 0.876 AC XY: 65158 AN XY: 74420

Gnomad4 AFR AF: 0.970

Gnomad4 AMR AF: 0.827

Gnomad4 ASJ AF: 0.876

Gnomad4 EAS AF: 0.838

Gnomad4 SAS AF: 0.817

Gnomad4 FIN AF: 0.835

Gnomad4 NFE AF: 0.844

Gnomad4 OTH AF: 0.854

Alfa AF: 0.849 Hom.: 58374

Bravo AF: 0.879

Asia WGS AF: 0.831 AC: 2892 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.13
DANN	Benign	0.77

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: rs472926; hg19: chr11-125905258;