chr11-126003207-G-A

Position:

• chr11-126003207-G-A

Variant summary

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

The NM_001378964.1(CDON):​c.2026+695C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.561 in 152,012 control chromosomes in the GnomAD database, including 24,278 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 0.56 (24278 hom., cov: 32)
• Consequence: CDON NM_001378964.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.21

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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.795 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CDON	NM_001378964.1	c.2026+695C>T		intron_variant		ENST00000531738.6	NP_001365893.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CDON	ENST00000531738.6	c.2026+695C>T		intron_variant		1	NM_001378964.1	ENSP00000432901	P1

Frequencies

GnomAD3 genomes AF: 0.561 AC: 85244 AN: 151894 Hom.: 24256 Cov.: 32

Gnomad AFR AF: 0.578

Gnomad AMI AF: 0.487

Gnomad AMR AF: 0.566

Gnomad ASJ AF: 0.527

Gnomad EAS AF: 0.814

Gnomad SAS AF: 0.642

Gnomad FIN AF: 0.497

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.537

Gnomad OTH AF: 0.580

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

GnomAD4 genome AF: 0.561 AC: 85305 AN: 152012 Hom.: 24278 Cov.: 32 AF XY: 0.561 AC XY: 41647 AN XY: 74286

Gnomad4 AFR AF: 0.578

Gnomad4 AMR AF: 0.566

Gnomad4 ASJ AF: 0.527

Gnomad4 EAS AF: 0.815

Gnomad4 SAS AF: 0.643

Gnomad4 FIN AF: 0.497

Gnomad4 NFE AF: 0.537

Gnomad4 OTH AF: 0.576

Alfa AF: 0.548 Hom.: 44920

Bravo AF: 0.571

Asia WGS AF: 0.650 AC: 2259 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.069
DANN	Benign	0.47

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: rs7104745; hg19: chr11-125873102;