Variant chr16-83678282-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_001257.5(CDH13):c.1359C>T(p.Asp453Asp) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0396 in 1,613,856 control chromosomes in the GnomAD database, including 1,819 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.063 ( 463 hom., cov: 32)

Exomes 𝑓: 0.037 ( 1356 hom. )

Consequence

CDH13
NM_001257.5 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: -1.95

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:

LOC124900603 (HGNC:):

LOC124900603 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.71).

BP6

Variant 16-83678282-C-T is Benign according to our data. Variant chr16-83678282-C-T is described in ClinVar as [Benign]. Clinvar id is 257643.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-1.95 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.126 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CDH13	NM_001257.5 linkuse as main transcript	c.1359C>T	p.Asp453Asp	synonymous_variant	10/14	ENST00000567109.6	NP_001248.1	P55290-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CDH13	ENST00000567109.6 linkuse as main transcript	c.1359C>T	p.Asp453Asp	synonymous_variant	10/14	1	NM_001257.5	ENSP00000479395.1		P55290-1

Frequencies

GnomAD3 genomes

AF:

0.0631

AC:

9592

AN:

152066

Hom.:

461

Cov.:

show subpopulations

Gnomad AFR

AF:

0.129

Gnomad AMI

AF:

0.0308

Gnomad AMR

AF:

0.0375

Gnomad ASJ

AF:

0.0412

Gnomad EAS

AF:

0.00212

Gnomad SAS

AF:

0.0475

Gnomad FIN

AF:

0.0873

Gnomad MID

AF:

0.0506

Gnomad NFE

AF:

0.0329

Gnomad OTH

AF:

0.0475

GnomAD3 exomes

AF:

0.0429

AC:

10684

AN:

249166

Hom.:

395

AF XY:

0.0423

AC XY:

5718

AN XY:

135182

show subpopulations

Gnomad AFR exome

AF:

0.133

Gnomad AMR exome

AF:

0.0233

Gnomad ASJ exome

AF:

0.0434

Gnomad EAS exome

AF:

0.00223

Gnomad SAS exome

AF:

0.0497

Gnomad FIN exome

AF:

0.0829

Gnomad NFE exome

AF:

0.0339

Gnomad OTH exome

AF:

0.0357

GnomAD4 exome

AF:

0.0371

AC:

54242

AN:

1461672

Hom.:

1356

Cov.:

AF XY:

0.0371

AC XY:

26993

AN XY:

727124

show subpopulations

Gnomad4 AFR exome

AF:

0.135

Gnomad4 AMR exome

AF:

0.0255

Gnomad4 ASJ exome

AF:

0.0422

Gnomad4 EAS exome

AF:

0.00128

Gnomad4 SAS exome

AF:

0.0472

Gnomad4 FIN exome

AF:

0.0783

Gnomad4 NFE exome

AF:

0.0330

Gnomad4 OTH exome

AF:

0.0385

GnomAD4 genome

AF:

0.0632

AC:

9611

AN:

152184

Hom.:

463

Cov.:

AF XY:

0.0652

AC XY:

4853

AN XY:

74408

show subpopulations

Gnomad4 AFR

AF:

0.129

Gnomad4 AMR

AF:

0.0375

Gnomad4 ASJ

AF:

0.0412

Gnomad4 EAS

AF:

0.00232

Gnomad4 SAS

AF:

0.0479

Gnomad4 FIN

AF:

0.0873

Gnomad4 NFE

AF:

0.0329

Gnomad4 OTH

AF:

0.0470

Alfa

AF:

0.0417

Hom.:

135

Bravo

AF:

0.0622

Asia WGS

AF:

0.0370

AC:

128

AN:

3478

EpiCase

AF:

0.0320

EpiControl

AF:

0.0354

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 10, 2021	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.71

CADD

Benign

0.096

DANN

Benign

0.55

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