Variant chr11-125956807-G-A details in Genebe, Genetics Data Aggregator

Variant summary

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

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

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 1.03

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:

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]

VSIG10L2 links:

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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=-0.91).

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_multiple_submitters_no_conflicts, 2 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 linkuse as main transcript			downstream_gene_variant		ENST00000531738.6

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CDON	ENST00000392693.7 linkuse as main transcript	c.*4135C>T	3_prime_UTR_variant	20/20	1			Q4KMG0-1
VSIG10L2	ENST00000638636.2 linkuse as main transcript	c.*893G>A	3_prime_UTR_variant	10/10	5		A2
CDON	ENST00000684078.1 linkuse as main transcript	c.*4135C>T	3_prime_UTR_variant	20/20				Q4KMG0-1
CDON	ENST00000531738.6 linkuse as main transcript		downstream_gene_variant		1	NM_001378964.1	P1	Q4KMG0-2

Frequencies

GnomAD3 genomes

AF:

0.491

AC:

74575

AN:

151888

Hom.:

19117

Cov.:

show subpopulations

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.:

AF XY:

0.531

AC XY:

205419

AN XY:

386672

show subpopulations

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.:

AF XY:

0.496

AC XY:

36860

AN XY:

74280

show subpopulations

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:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Holoprosencephaly sequence

Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

not provided

Benign:1

Benign, criteria provided, single submitter

not provided

Breakthrough Genomics, Breakthrough Genomics

- -

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

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