Variant chr11-125957177-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 NM_001378964.1(CDON):c.*3765C>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 0.205 in 152,178 control chromosomes in the GnomAD database, including 3,439 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.21 ( 3438 hom., cov: 32)

Exomes 𝑓: 0.13 ( 1 hom. )

Consequence

CDON
NM_001378964.1 3_prime_UTR

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.646

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=-0.86).

BP6

Variant 11-125957177-G-A is Benign according to our data. Variant chr11-125957177-G-A is described in ClinVar as [Benign]. Clinvar id is 303381.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.406 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CDON	NM_001378964.1 linkuse as main transcript	c.*3765C>T		3_prime_UTR_variant	20/20	ENST00000531738.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CDON	ENST00000531738.6 linkuse as main transcript	c.*3765C>T		3_prime_UTR_variant	20/20	1	NM_001378964.1	P1	Q4KMG0-2

Frequencies

GnomAD3 genomes

AF:

0.206

AC:

31243

AN:

151940

Hom.:

3439

Cov.:

show subpopulations

Gnomad AFR

AF:

0.196

Gnomad AMI

AF:

0.138

Gnomad AMR

AF:

0.190

Gnomad ASJ

AF:

0.196

Gnomad EAS

AF:

0.420

Gnomad SAS

AF:

0.206

Gnomad FIN

AF:

0.218

Gnomad MID

AF:

0.213

Gnomad NFE

AF:

0.198

Gnomad OTH

AF:

0.224

GnomAD4 exome

AF:

0.125

AC:

AN:

120

Hom.:

Cov.:

AF XY:

0.118

AC XY:

AN XY:

show subpopulations

Gnomad4 AFR exome

AF:

0.500

Gnomad4 FIN exome

AF:

0.167

Gnomad4 NFE exome

AF:

0.0980

Gnomad4 OTH exome

AF:

0.333

GnomAD4 genome

AF:

0.206

AC:

31248

AN:

152058

Hom.:

3438

Cov.:

AF XY:

0.208

AC XY:

15431

AN XY:

74304

show subpopulations

Gnomad4 AFR

AF:

0.195

Gnomad4 AMR

AF:

0.190

Gnomad4 ASJ

AF:

0.196

Gnomad4 EAS

AF:

0.420

Gnomad4 SAS

AF:

0.207

Gnomad4 FIN

AF:

0.218

Gnomad4 NFE

AF:

0.198

Gnomad4 OTH

AF:

0.222

Alfa

AF:

0.200

Hom.:

2058

Bravo

AF:

0.204

Asia WGS

AF:

0.277

AC:

962

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

not provided

Breakthrough Genomics, Breakthrough Genomics

- -

Holoprosencephaly 11

Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jan 13, 2018

This 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

-0.86

CADD

Benign

1.8

DANN

Benign

0.59

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