11-125956807-G-A

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The ENST00000392693.7(CDON):c.*4135C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.525 in 988,828 control chromosomes in the GnomAD database, including 137,925 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.49 (19124 hom., cov: 32)
  • Exomes 𝑓: 0.53 (118801 hom.)
• Consequence: CDON ENST00000392693.7 3_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.03

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]

VSIG10L2 (HGNC:27879): (V-set and immunoglobulin domain containing 10 like 2) Predicted to enable cell adhesion molecule binding activity. Predicted to be involved in cell-cell adhesion. Predicted to be active in cell-cell junction. Predicted to be integral component of plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BP6: Variant 11-125956807-G-A is Benign according to our data. Variant chr11-125956807-G-A is described in ClinVar as [Benign]. Clinvar id is 368942.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.688 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CDON	NM_001378964.1			downstream_gene_variant		ENST00000531738.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CDON	ENST00000392693.7	c.*4135C>T		3_prime_UTR_variant	20/20	1
VSIG10L2	ENST00000638636.2	c.*893G>A		3_prime_UTR_variant	10/10	5		A2
CDON	ENST00000684078.1	c.*4135C>T		3_prime_UTR_variant	20/20
CDON	ENST00000531738.6			downstream_gene_variant		1	NM_001378964.1	P1

Frequencies

GnomAD3 genomes AF: 0.491 AC: 74575 AN: 151888 Hom.: 19117 Cov.: 32

Gnomad AFR AF: 0.351

Gnomad AMI AF: 0.454

Gnomad AMR AF: 0.473

Gnomad ASJ AF: 0.559

Gnomad EAS AF: 0.707

Gnomad SAS AF: 0.523

Gnomad FIN AF: 0.621

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.538

Gnomad OTH AF: 0.506

GnomAD4 exome AF: 0.531 AC: 444740 AN: 836822 Hom.: 118801 Cov.: 33 AF XY: 0.531 AC XY: 205419 AN XY: 386672

Gnomad4 AFR exome AF: 0.335

Gnomad4 AMR exome AF: 0.431

Gnomad4 ASJ exome AF: 0.552

Gnomad4 EAS exome AF: 0.714

Gnomad4 SAS exome AF: 0.520

Gnomad4 FIN exome AF: 0.579

Gnomad4 NFE exome AF: 0.535

Gnomad4 OTH exome AF: 0.538

GnomAD4 genome AF: 0.491 AC: 74609 AN: 152006 Hom.: 19124 Cov.: 32 AF XY: 0.496 AC XY: 36860 AN XY: 74280

Gnomad4 AFR AF: 0.351

Gnomad4 AMR AF: 0.473

Gnomad4 ASJ AF: 0.559

Gnomad4 EAS AF: 0.707

Gnomad4 SAS AF: 0.523

Gnomad4 FIN AF: 0.621

Gnomad4 NFE AF: 0.538

Gnomad4 OTH AF: 0.503

Alfa AF: 0.536 Hom.: 20686

Bravo AF: 0.477

Asia WGS AF: 0.567 AC: 1968 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

Holoprosencephaly sequence Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	5.3
Dann	Benign	0.60

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs4937076; hg19: chr11-125826702;