chr11-125957112-C-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_001378964.1(CDON):​c.*3830G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0228 in 153,066 control chromosomes in the GnomAD database, including 150 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.023 ( 150 hom., cov: 32)
Exomes 𝑓: 0.0035 ( 0 hom. )

Consequence

CDON
NM_001378964.1 3_prime_UTR

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.628
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BP6
Variant 11-125957112-C-T is Benign according to our data. Variant chr11-125957112-C-T is described in ClinVar as [Benign]. Clinvar id is 303380.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0771 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
CDONNM_001378964.1 linkuse as main transcriptc.*3830G>A 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.*3830G>A 3_prime_UTR_variant 20/201 NM_001378964.1 P1Q4KMG0-2
CDONENST00000392693.7 linkuse as main transcriptc.*3830G>A 3_prime_UTR_variant 20/201 Q4KMG0-1
VSIG10L2ENST00000638636.2 linkuse as main transcriptc.*1198C>T 3_prime_UTR_variant 10/105 A2
CDONENST00000684078.1 linkuse as main transcriptc.*3830G>A 3_prime_UTR_variant 20/20 Q4KMG0-1

Frequencies

GnomAD3 genomes
AF:
0.0228
AC:
3475
AN:
152082
Hom.:
149
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0794
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00917
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000623
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000309
Gnomad OTH
AF:
0.0129
GnomAD4 exome
AF:
0.00346
AC:
3
AN:
866
Hom.:
0
Cov.:
3
AF XY:
0.00446
AC XY:
2
AN XY:
448
show subpopulations
Gnomad4 AFR exome
AF:
0.188
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
AF:
0.0229
AC:
3486
AN:
152200
Hom.:
150
Cov.:
32
AF XY:
0.0219
AC XY:
1629
AN XY:
74436
show subpopulations
Gnomad4 AFR
AF:
0.0794
Gnomad4 AMR
AF:
0.00909
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000624
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000309
Gnomad4 OTH
AF:
0.0128
Alfa
AF:
0.0111
Hom.:
10
Bravo
AF:
0.0262
Asia WGS
AF:
0.00404
AC:
14
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
-0.89
CADD
Benign
0.69
DANN
Benign
0.70

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: rs116746244; hg19: chr11-125827007; API