rs1433157

Positions:

• chr16-82644618-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001257.5(CDH13):​c.45+17481T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.514 in 151,930 control chromosomes in the GnomAD database, including 20,787 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 0.51 (20787 hom., cov: 31)
• Consequence: CDH13 NM_001257.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0140

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.638 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CDH13	NM_001257.5	c.45+17481T>C		intron_variant		ENST00000567109.6	NP_001248.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CDH13	ENST00000567109.6	c.45+17481T>C		intron_variant		1	NM_001257.5	ENSP00000479395.1

Frequencies

GnomAD3 genomes AF: 0.514 AC: 78042 AN: 151812 Hom.: 20746 Cov.: 31

Gnomad AFR AF: 0.644

Gnomad AMI AF: 0.404

Gnomad AMR AF: 0.511

Gnomad ASJ AF: 0.543

Gnomad EAS AF: 0.335

Gnomad SAS AF: 0.383

Gnomad FIN AF: 0.422

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.473

Gnomad OTH AF: 0.507

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.514 AC: 78136 AN: 151930 Hom.: 20787 Cov.: 31 AF XY: 0.509 AC XY: 37794 AN XY: 74258

Gnomad4 AFR AF: 0.645

Gnomad4 AMR AF: 0.512

Gnomad4 ASJ AF: 0.543

Gnomad4 EAS AF: 0.335

Gnomad4 SAS AF: 0.383

Gnomad4 FIN AF: 0.422

Gnomad4 NFE AF: 0.473

Gnomad4 OTH AF: 0.501

Alfa AF: 0.472 Hom.: 22288

Bravo AF: 0.529

Asia WGS AF: 0.334 AC: 1168 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	2.2
DANN	Benign	0.66

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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

Other links and lift over

dbSNP: rs1433157; hg19: chr16-82678223;