16-82792902-C-G

Variant summary

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

The NM_001257.5(CDH13):​c.46-65460C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.069 in 148,682 control chromosomes in the GnomAD database, including 441 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 0.069 ( 441 hom., cov: 34)

Consequence

CDH13
NM_001257.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0300

Publications

2 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=-0.75).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0946 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CDH13NM_001257.5 linkc.46-65460C>G intron_variant Intron 1 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.46-65460C>G intron_variant Intron 1 of 13 1 NM_001257.5 ENSP00000479395.1 P55290-1

Frequencies

GnomAD3 genomes
AF:
0.0690
AC:
10252
AN:
148564
Hom.:
438
Cov.:
34
show subpopulations
Gnomad AFR
AF:
0.0271
Gnomad AMI
AF:
0.0447
Gnomad AMR
AF:
0.0860
Gnomad ASJ
AF:
0.134
Gnomad EAS
AF:
0.0308
Gnomad SAS
AF:
0.102
Gnomad FIN
AF:
0.0675
Gnomad MID
AF:
0.106
Gnomad NFE
AF:
0.0875
Gnomad OTH
AF:
0.104
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0690
AC:
10255
AN:
148682
Hom.:
441
Cov.:
34
AF XY:
0.0677
AC XY:
4904
AN XY:
72458
show subpopulations
African (AFR)
AF:
0.0271
AC:
1103
AN:
40752
American (AMR)
AF:
0.0860
AC:
1285
AN:
14938
Ashkenazi Jewish (ASJ)
AF:
0.134
AC:
458
AN:
3424
East Asian (EAS)
AF:
0.0313
AC:
161
AN:
5150
South Asian (SAS)
AF:
0.102
AC:
449
AN:
4386
European-Finnish (FIN)
AF:
0.0675
AC:
687
AN:
10176
Middle Eastern (MID)
AF:
0.104
AC:
30
AN:
288
European-Non Finnish (NFE)
AF:
0.0875
AC:
5829
AN:
66618
Other (OTH)
AF:
0.104
AC:
213
AN:
2056
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.506
Heterozygous variant carriers
0
492
984
1475
1967
2459
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
118
236
354
472
590
<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:
0.0230
Hom.:
6
Bravo
AF:
0.0684
Asia WGS
AF:
0.0630
AC:
219
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.75
CADD
Benign
2.4
DANN
Benign
0.74
PhyloP100
-0.030
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: rs17192646; hg19: chr16-82826507; API