Variant chr16-83032360-T-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_001257.5(CDH13):c.366+142T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.54 in 650,656 control chromosomes in the GnomAD database, including 96,200 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.54 ( 22360 hom., cov: 32)

Exomes 𝑓: 0.54 ( 73840 hom. )

Consequence

CDH13
NM_001257.5 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.0690

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 -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BP6

Variant 16-83032360-T-A is Benign according to our data. Variant chr16-83032360-T-A is described in ClinVar as [Benign]. Clinvar id is 1244376.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.559 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.366+142T>A		intron_variant		ENST00000567109.6	NP_001248.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CDH13	ENST00000567109.6 linkuse as main transcript	c.366+142T>A		intron_variant		1	NM_001257.5	ENSP00000479395	P1	P55290-1

Frequencies

GnomAD3 genomes

AF:

0.541

AC:

82177

AN:

151900

Hom.:

22327

Cov.:

show subpopulations

Gnomad AFR

AF:

0.524

Gnomad AMI

AF:

0.643

Gnomad AMR

AF:

0.539

Gnomad ASJ

AF:

0.438

Gnomad EAS

AF:

0.449

Gnomad SAS

AF:

0.578

Gnomad FIN

AF:

0.636

Gnomad MID

AF:

0.519

Gnomad NFE

AF:

0.546

Gnomad OTH

AF:

0.516

GnomAD4 exome

AF:

0.539

AC:

268799

AN:

498638

Hom.:

73840

Cov.:

AF XY:

0.540

AC XY:

139641

AN XY:

258644

show subpopulations

Gnomad4 AFR exome

AF:

0.524

Gnomad4 AMR exome

AF:

0.537

Gnomad4 ASJ exome

AF:

0.444

Gnomad4 EAS exome

AF:

0.448

Gnomad4 SAS exome

AF:

0.578

Gnomad4 FIN exome

AF:

0.624

Gnomad4 NFE exome

AF:

0.540

Gnomad4 OTH exome

AF:

0.533

GnomAD4 genome

AF:

0.541

AC:

82273

AN:

152018

Hom.:

22360

Cov.:

AF XY:

0.545

AC XY:

40493

AN XY:

74274

show subpopulations

Gnomad4 AFR

AF:

0.524

Gnomad4 AMR

AF:

0.539

Gnomad4 ASJ

AF:

0.438

Gnomad4 EAS

AF:

0.450

Gnomad4 SAS

AF:

0.577

Gnomad4 FIN

AF:

0.636

Gnomad4 NFE

AF:

0.546

Gnomad4 OTH

AF:

0.520

Alfa

AF:

0.541

Hom.:

2754

Bravo

AF:

0.530

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
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

-0.90

CADD

Benign

1.6

DANN

Benign

0.73

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