Variant 11-125995077-AAACAAC-AAAC details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1

The NM_001378964.1(CDON):c.2363-28_2363-26delGTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.264 in 1,565,838 control chromosomes in the GnomAD database, including 58,667 homozygotes. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.24 ( 4827 hom., cov: 25)

Exomes 𝑓: 0.27 ( 53840 hom. )

Consequence

CDON
NM_001378964.1 intron

Scores

Not classified

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 2.44

Variant links:

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]

CDON links:

CDON (HGNC:):

CDON links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP6

Variant 11-125995077-AAAC-A is Benign according to our data. Variant chr11-125995077-AAAC-A is described in ClinVar as [Likely_benign]. Clinvar id is 260787.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.463 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CDON	NM_001378964.1 linkuse as main transcript	c.2363-28_2363-26delGTT		intron_variant		ENST00000531738.6	NP_001365893.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CDON	ENST00000531738.6 linkuse as main transcript	c.2363-28_2363-26delGTT		intron_variant		1	NM_001378964.1	ENSP00000432901.2		Q4KMG0-2E9PN78

Frequencies

GnomAD3 genomes

AF:

0.243

AC:

36890

AN:

151892

Hom.:

4827

Cov.:

show subpopulations

Gnomad AFR

AF:

0.151

Gnomad AMI

AF:

0.228

Gnomad AMR

AF:

0.276

Gnomad ASJ

AF:

0.228

Gnomad EAS

AF:

0.477

Gnomad SAS

AF:

0.282

Gnomad FIN

AF:

0.245

Gnomad MID

AF:

0.253

Gnomad NFE

AF:

0.270

Gnomad OTH

AF:

0.281

GnomAD3 exomes

AF:

0.277

AC:

68414

AN:

246792

Hom.:

9983

AF XY:

0.279

AC XY:

37366

AN XY:

133834

show subpopulations

Gnomad AFR exome

AF:

0.149

Gnomad AMR exome

AF:

0.307

Gnomad ASJ exome

AF:

0.225

Gnomad EAS exome

AF:

0.479

Gnomad SAS exome

AF:

0.269

Gnomad FIN exome

AF:

0.231

Gnomad NFE exome

AF:

0.269

Gnomad OTH exome

AF:

0.282

GnomAD4 exome

AF:

0.267

AC:

377174

AN:

1413828

Hom.:

53840

AF XY:

0.268

AC XY:

189309

AN XY:

706356

show subpopulations

Gnomad4 AFR exome

AF:

0.143

Gnomad4 AMR exome

AF:

0.305

Gnomad4 ASJ exome

AF:

0.225

Gnomad4 EAS exome

AF:

0.501

Gnomad4 SAS exome

AF:

0.267

Gnomad4 FIN exome

AF:

0.239

Gnomad4 NFE exome

AF:

0.263

Gnomad4 OTH exome

AF:

0.263

GnomAD4 genome

AF:

0.243

AC:

36897

AN:

152010

Hom.:

4827

Cov.:

AF XY:

0.244

AC XY:

18134

AN XY:

74294

show subpopulations

Gnomad4 AFR

AF:

0.151

Gnomad4 AMR

AF:

0.277

Gnomad4 ASJ

AF:

0.228

Gnomad4 EAS

AF:

0.478

Gnomad4 SAS

AF:

0.283

Gnomad4 FIN

AF:

0.245

Gnomad4 NFE

AF:

0.270

Gnomad4 OTH

AF:

0.278

Bravo

AF:

0.246

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

- -

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Aug 23, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over