Variant 16-83032059-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BA1

The NM_001257.5(CDH13):c.207G>A(p.Ser69=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.543 in 1,607,566 control chromosomes in the GnomAD database, including 238,124 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.54 ( 22572 hom., cov: 32)

Exomes 𝑓: 0.54 ( 215552 hom. )

Consequence

CDH13
NM_001257.5 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.166

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 -19 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.43).

BP6

Variant 16-83032059-G-A is Benign according to our data. Variant chr16-83032059-G-A is described in ClinVar as [Benign]. Clinvar id is 257649.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-0.166 with no splicing effect.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.554 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.207G>A	p.Ser69=	synonymous_variant	3/14	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.207G>A	p.Ser69=	synonymous_variant	3/14	1	NM_001257.5	ENSP00000479395	P1	P55290-1

Frequencies

GnomAD3 genomes

AF:

0.543

AC:

82560

AN:

151910

Hom.:

22539

Cov.:

show subpopulations

Gnomad AFR

AF:

0.540

Gnomad AMI

AF:

0.644

Gnomad AMR

AF:

0.534

Gnomad ASJ

AF:

0.435

Gnomad EAS

AF:

0.442

Gnomad SAS

AF:

0.573

Gnomad FIN

AF:

0.637

Gnomad MID

AF:

0.509

Gnomad NFE

AF:

0.544

Gnomad OTH

AF:

0.516

GnomAD3 exomes

AF:

0.542

AC:

129800

AN:

239634

Hom.:

35300

AF XY:

0.544

AC XY:

70479

AN XY:

129648

show subpopulations

Gnomad AFR exome

AF:

0.546

Gnomad AMR exome

AF:

0.530

Gnomad ASJ exome

AF:

0.441

Gnomad EAS exome

AF:

0.445

Gnomad SAS exome

AF:

0.567

Gnomad FIN exome

AF:

0.636

Gnomad NFE exome

AF:

0.546

Gnomad OTH exome

AF:

0.514

GnomAD4 exome

AF:

0.543

AC:

790597

AN:

1455536

Hom.:

215552

Cov.:

AF XY:

0.543

AC XY:

392860

AN XY:

723424

show subpopulations

Gnomad4 AFR exome

AF:

0.538

Gnomad4 AMR exome

AF:

0.530

Gnomad4 ASJ exome

AF:

0.443

Gnomad4 EAS exome

AF:

0.435

Gnomad4 SAS exome

AF:

0.571

Gnomad4 FIN exome

AF:

0.627

Gnomad4 NFE exome

AF:

0.545

Gnomad4 OTH exome

AF:

0.533

GnomAD4 genome

AF:

0.544

AC:

82658

AN:

152030

Hom.:

22572

Cov.:

AF XY:

0.548

AC XY:

40680

AN XY:

74280

show subpopulations

Gnomad4 AFR

AF:

0.541

Gnomad4 AMR

AF:

0.534

Gnomad4 ASJ

AF:

0.435

Gnomad4 EAS

AF:

0.442

Gnomad4 SAS

AF:

0.572

Gnomad4 FIN

AF:

0.637

Gnomad4 NFE

AF:

0.544

Gnomad4 OTH

AF:

0.520

Alfa

AF:

0.528

Hom.:

34220

Bravo

AF:

0.533

Asia WGS

AF:

0.541

AC:

1880

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

- -

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

-0.43

CADD

Benign

9.1

DANN

Benign

0.89

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