chr11-125957058-A-C

Variant summary

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

The NM_001378964.1(CDON):​c.*3884T>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.292 in 164,026 control chromosomes in the GnomAD database, including 7,494 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.29 ( 7034 hom., cov: 32)
Exomes 𝑓: 0.27 ( 460 hom. )

Consequence

CDON
NM_001378964.1 3_prime_UTR

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.519
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]
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BP6
Variant 11-125957058-A-C is Benign according to our data. Variant chr11-125957058-A-C is described in ClinVar as [Benign]. Clinvar id is 303378.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.337 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
CDONNM_001378964.1 linkuse as main transcriptc.*3884T>G 3_prime_UTR_variant 20/20 ENST00000531738.6

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CDONENST00000531738.6 linkuse as main transcriptc.*3884T>G 3_prime_UTR_variant 20/201 NM_001378964.1 P1Q4KMG0-2
CDONENST00000392693.7 linkuse as main transcriptc.*3884T>G 3_prime_UTR_variant 20/201 Q4KMG0-1
VSIG10L2ENST00000638636.2 linkuse as main transcriptc.*1144A>C 3_prime_UTR_variant 10/105 A2
CDONENST00000684078.1 linkuse as main transcriptc.*3884T>G 3_prime_UTR_variant 20/20 Q4KMG0-1

Frequencies

GnomAD3 genomes
AF:
0.294
AC:
44685
AN:
151954
Hom.:
7023
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.186
Gnomad AMI
AF:
0.319
Gnomad AMR
AF:
0.285
Gnomad ASJ
AF:
0.362
Gnomad EAS
AF:
0.290
Gnomad SAS
AF:
0.317
Gnomad FIN
AF:
0.403
Gnomad MID
AF:
0.307
Gnomad NFE
AF:
0.340
Gnomad OTH
AF:
0.287
GnomAD4 exome
AF:
0.270
AC:
3233
AN:
11954
Hom.:
460
Cov.:
4
AF XY:
0.274
AC XY:
1606
AN XY:
5860
show subpopulations
Gnomad4 AFR exome
AF:
0.162
Gnomad4 AMR exome
AF:
0.400
Gnomad4 ASJ exome
AF:
0.304
Gnomad4 EAS exome
AF:
0.224
Gnomad4 SAS exome
AF:
0.246
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.274
Gnomad4 OTH exome
AF:
0.243
GnomAD4 genome
AF:
0.294
AC:
44727
AN:
152072
Hom.:
7034
Cov.:
32
AF XY:
0.297
AC XY:
22043
AN XY:
74314
show subpopulations
Gnomad4 AFR
AF:
0.186
Gnomad4 AMR
AF:
0.285
Gnomad4 ASJ
AF:
0.362
Gnomad4 EAS
AF:
0.290
Gnomad4 SAS
AF:
0.317
Gnomad4 FIN
AF:
0.403
Gnomad4 NFE
AF:
0.340
Gnomad4 OTH
AF:
0.286
Alfa
AF:
0.320
Hom.:
2187
Bravo
AF:
0.284
Asia WGS
AF:
0.293
AC:
1019
AN:
3478

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

Holoprosencephaly 11 Benign:1
Benign, criteria provided, single submitterclinical testingIllumina Laboratory Services, IlluminaJan 13, 2018This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.85
CADD
Benign
4.2
DANN
Benign
0.41

Splicing

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.

Other links and lift over

dbSNP: rs13424; hg19: chr11-125826953; API