Genetic Variant CDON:c.2362+49C>A (chr11-125997158-G-T) – ACMG Classification: Benign (-20 pts)

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001378964.1(CDON):c.2362+49C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.926 in 1,297,830 control chromosomes in the GnomAD database, including 556,490 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.93 ( 65617 hom., cov: 32)

Exomes 𝑓: 0.93 ( 490873 hom. )

Consequence

CDON
NM_001378964.1 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: -2.78

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-1.0).

BP6

Variant 11-125997158-G-T is Benign according to our data. Variant chr11-125997158-G-T is described in ClinVar as [Benign]. Clinvar id is 260786.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.972 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CDON	NM_001378964.1 link	c.2362+49C>A		intron_variant	Intron 12 of 19	ENST00000531738.6	NP_001365893.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CDON	ENST00000531738.6 link	c.2362+49C>A		intron_variant	Intron 12 of 19	1	NM_001378964.1	ENSP00000432901.2		Q4KMG0-2E9PN78

Frequencies

GnomAD3 genomes

AF:

0.928

AC:

141142

AN:

152042

Hom.:

65553

Cov.:

show subpopulations

Gnomad AFR

AF:

0.927

Gnomad AMI

AF:

0.974

Gnomad AMR

AF:

0.947

Gnomad ASJ

AF:

0.907

Gnomad EAS

AF:

0.995

Gnomad SAS

AF:

0.918

Gnomad FIN

AF:

0.937

Gnomad MID

AF:

0.892

Gnomad NFE

AF:

0.921

Gnomad OTH

AF:

0.918

GnomAD3 exomes

AF:

0.931

AC:

229870

AN:

246864

Hom.:

107084

AF XY:

0.930

AC XY:

124302

AN XY:

133674

show subpopulations

Gnomad AFR exome

AF:

0.925

Gnomad AMR exome

AF:

0.962

Gnomad ASJ exome

AF:

0.905

Gnomad EAS exome

AF:

0.995

Gnomad SAS exome

AF:

0.917

Gnomad FIN exome

AF:

0.933

Gnomad NFE exome

AF:

0.918

Gnomad OTH exome

AF:

0.929

GnomAD4 exome

AF:

0.925

AC:

1060225

AN:

1145670

Hom.:

490873

Cov.:

AF XY:

0.925

AC XY:

541851

AN XY:

585918

show subpopulations

Gnomad4 AFR exome

AF:

0.925

Gnomad4 AMR exome

AF:

0.960

Gnomad4 ASJ exome

AF:

0.908

Gnomad4 EAS exome

AF:

0.998

Gnomad4 SAS exome

AF:

0.918

Gnomad4 FIN exome

AF:

0.930

Gnomad4 NFE exome

AF:

0.921

Gnomad4 OTH exome

AF:

0.925

GnomAD4 genome

AF:

0.928

AC:

141266

AN:

152160

Hom.:

65617

Cov.:

AF XY:

0.929

AC XY:

69123

AN XY:

74396

show subpopulations

Gnomad4 AFR

AF:

0.927

Gnomad4 AMR

AF:

0.947

Gnomad4 ASJ

AF:

0.907

Gnomad4 EAS

AF:

0.995

Gnomad4 SAS

AF:

0.919

Gnomad4 FIN

AF:

0.937

Gnomad4 NFE

AF:

0.921

Gnomad4 OTH

AF:

0.918

Alfa

AF:

0.909

Hom.:

6540

Bravo

AF:

0.930

Asia WGS

AF:

0.958

AC:

3334

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Nov 10, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

not specified

Benign:1

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Holoprosencephaly 11

Benign:1

Jul 22, 2021

Genome-Nilou Lab

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

-1.0

CADD

Benign

0.36

DANN

Benign

0.35

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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