Variant chr16-83031886-G-C details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_001257.5(CDH13):c.158-124G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.105 in 742,346 control chromosomes in the GnomAD database, including 4,387 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.12 ( 1144 hom., cov: 32)

Exomes 𝑓: 0.10 ( 3243 hom. )

Consequence

CDH13
NM_001257.5 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.05

Variant links:

Genes affected

CDH13 (HGNC:1753): (cadherin 13) This gene encodes a member of the cadherin superfamily. The encoded protein is localized to the surface of the cell membrane and is anchored by a GPI moiety, rather than by a transmembrane domain. The protein lacks the cytoplasmic domain characteristic of other cadherins, and so is not thought to be a cell-cell adhesion glycoprotein. This protein acts as a negative regulator of axon growth during neural differentiation. It also protects vascular endothelial cells from apoptosis due to oxidative stress, and is associated with resistance to atherosclerosis. The gene is hypermethylated in many types of cancer. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, May 2011]

CDH13 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.88).

BP6

Variant 16-83031886-G-C is Benign according to our data. Variant chr16-83031886-G-C is described in ClinVar as [Benign]. Clinvar id is 1239670.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.164 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CDH13	NM_001257.5 link	c.158-124G>C		intron_variant		ENST00000567109.6	NP_001248.1	P55290-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CDH13	ENST00000567109.6 link	c.158-124G>C		intron_variant		1	NM_001257.5	ENSP00000479395.1		P55290-1

Frequencies

GnomAD3 genomes

AF:

0.117

AC:

17845

AN:

152040

Hom.:

1143

Cov.:

show subpopulations

Gnomad AFR

AF:

0.167

Gnomad AMI

AF:

0.149

Gnomad AMR

AF:

0.0787

Gnomad ASJ

AF:

0.114

Gnomad EAS

AF:

0.0521

Gnomad SAS

AF:

0.108

Gnomad FIN

AF:

0.116

Gnomad MID

AF:

0.104

Gnomad NFE

AF:

0.102

Gnomad OTH

AF:

0.109

GnomAD4 exome

AF:

0.102

AC:

60032

AN:

590188

Hom.:

3243

AF XY:

0.102

AC XY:

31150

AN XY:

305412

show subpopulations

Gnomad4 AFR exome

AF:

0.168

Gnomad4 AMR exome

AF:

0.0661

Gnomad4 ASJ exome

AF:

0.115

Gnomad4 EAS exome

AF:

0.0726

Gnomad4 SAS exome

AF:

0.103

Gnomad4 FIN exome

AF:

0.117

Gnomad4 NFE exome

AF:

0.101

Gnomad4 OTH exome

AF:

0.104

GnomAD4 genome

AF:

0.117

AC:

17857

AN:

152158

Hom.:

1144

Cov.:

AF XY:

0.115

AC XY:

8589

AN XY:

74414

show subpopulations

Gnomad4 AFR

AF:

0.167

Gnomad4 AMR

AF:

0.0784

Gnomad4 ASJ

AF:

0.114

Gnomad4 EAS

AF:

0.0526

Gnomad4 SAS

AF:

0.107

Gnomad4 FIN

AF:

0.116

Gnomad4 NFE

AF:

0.102

Gnomad4 OTH

AF:

0.110

Alfa

AF:

0.0376

Hom.:

Bravo

AF:

0.116

Asia WGS

AF:

0.117

AC:

407

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 18, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

0.21

DANN

Benign

0.39

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

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