NM_001257.5:c.366+142T>A

Variant names:

Variant summary

Our verdict is Benign. The variant received -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

Publications

4 publications found

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:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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 CliVar as Benign. Clinvar id is 1244376.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-83032360-T-A is described in CliVar as Benign. Clinvar id is 1244376.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-83032360-T-A is described in CliVar as Benign. Clinvar id is 1244376.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-83032360-T-A is described in CliVar as Benign. Clinvar id is 1244376.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-83032360-T-A is described in CliVar as Benign. Clinvar id is 1244376.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-83032360-T-A is described in CliVar as Benign. Clinvar id is 1244376.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-83032360-T-A is described in CliVar as Benign. Clinvar id is 1244376.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-83032360-T-A is described in CliVar as Benign. Clinvar id is 1244376.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-83032360-T-A is described in CliVar as Benign. Clinvar id is 1244376.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-83032360-T-A is described in CliVar as Benign. Clinvar id is 1244376.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-83032360-T-A is described in CliVar 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 rank	MANE	Protein	UniProt
CDH13	NM_001257.5 link	c.366+142T>A		intron_variant	Intron 3 of 13	ENST00000567109.6	NP_001248.1	P55290-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CDH13	ENST00000567109.6 link	c.366+142T>A		intron_variant	Intron 3 of 13	1	NM_001257.5	ENSP00000479395.1		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

African (AFR)

AF:

0.524

AC:

6982

AN:

13330

American (AMR)

AF:

0.537

AC:

10119

AN:

18848

Ashkenazi Jewish (ASJ)

AF:

0.444

AC:

6207

AN:

13974

East Asian (EAS)

AF:

0.448

AC:

13945

AN:

31146

South Asian (SAS)

AF:

0.578

AC:

25172

AN:

43516

European-Finnish (FIN)

AF:

0.624

AC:

20274

AN:

32490

Middle Eastern (MID)

AF:

0.466

AC:

1309

AN:

2812

European-Non Finnish (NFE)

AF:

0.540

AC:

170069

AN:

314898

Other (OTH)

AF:

0.533

AC:

14722

AN:

27624

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.496

Heterozygous variant carriers

5732

11463

17195

22926

28658

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

1706

3412

5118

6824

8530

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.541

AC:

82273

AN:

152018

Hom.:

22360

Cov.:

AF XY:

0.545

AC XY:

40493

AN XY:

74274

show subpopulations

African (AFR)

AF:

0.524

AC:

21735

AN:

41450

American (AMR)

AF:

0.539

AC:

8233

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.438

AC:

1520

AN:

3470

East Asian (EAS)

AF:

0.450

AC:

2320

AN:

5160

South Asian (SAS)

AF:

0.577

AC:

2773

AN:

4808

European-Finnish (FIN)

AF:

0.636

AC:

6721

AN:

10560

Middle Eastern (MID)

AF:

0.537

AC:

158

AN:

294

European-Non Finnish (NFE)

AF:

0.546

AC:

37130

AN:

67982

Other (OTH)

AF:

0.520

AC:

1099

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1966

3932

5898

7864

9830

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

720

1440

2160

2880

3600

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

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

Breakthrough Genomics, Breakthrough Genomics

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:not provided

- -

Jun 18, 2021

GeneDx

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

1.6

(source)

DANN

Benign

0.73

PhyloP100

-0.069

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over