rs17284265

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001257.5(CDH13):​c.781+13682A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0874 in 152,206 control chromosomes in the GnomAD database, including 812 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.087 ( 812 hom., cov: 32)

Consequence

CDH13
NM_001257.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.00700

Publications

1 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]

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.13 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CDH13NM_001257.5 linkc.781+13682A>G intron_variant Intron 6 of 13 ENST00000567109.6 NP_001248.1 P55290-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CDH13ENST00000567109.6 linkc.781+13682A>G intron_variant Intron 6 of 13 1 NM_001257.5 ENSP00000479395.1 P55290-1

Frequencies

GnomAD3 genomes
AF:
0.0874
AC:
13299
AN:
152088
Hom.:
811
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0215
Gnomad AMI
AF:
0.138
Gnomad AMR
AF:
0.0672
Gnomad ASJ
AF:
0.0623
Gnomad EAS
AF:
0.000963
Gnomad SAS
AF:
0.0525
Gnomad FIN
AF:
0.147
Gnomad MID
AF:
0.0538
Gnomad NFE
AF:
0.133
Gnomad OTH
AF:
0.0848
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0874
AC:
13297
AN:
152206
Hom.:
812
Cov.:
32
AF XY:
0.0867
AC XY:
6452
AN XY:
74416
show subpopulations
African (AFR)
AF:
0.0214
AC:
889
AN:
41542
American (AMR)
AF:
0.0671
AC:
1026
AN:
15284
Ashkenazi Jewish (ASJ)
AF:
0.0623
AC:
216
AN:
3468
East Asian (EAS)
AF:
0.000965
AC:
5
AN:
5180
South Asian (SAS)
AF:
0.0523
AC:
252
AN:
4814
European-Finnish (FIN)
AF:
0.147
AC:
1560
AN:
10596
Middle Eastern (MID)
AF:
0.0544
AC:
16
AN:
294
European-Non Finnish (NFE)
AF:
0.133
AC:
9029
AN:
68006
Other (OTH)
AF:
0.0844
AC:
178
AN:
2110
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
616
1232
1847
2463
3079
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
160
320
480
640
800
<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:
0.108
Hom.:
141
Bravo
AF:
0.0782
Asia WGS
AF:
0.0220
AC:
78
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.87
CADD
Benign
1.5
DANN
Benign
0.65
PhyloP100
-0.0070
Mutation Taster
=100/0
polymorphism (auto)

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

Other links and lift over

dbSNP: rs17284265; hg19: chr16-83392293; API