rs17284098

Positions:

• chr16-83356473-A-G

Variant summary

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

The NM_001257.5(CDH13):​c.781+11467A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0865 in 152,166 control chromosomes in the GnomAD database, including 796 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 0.086 (796 hom., cov: 31)
• Consequence: CDH13 NM_001257.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.656

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.129 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CDH13	NM_001257.5	c.781+11467A>G		intron_variant		ENST00000567109.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CDH13	ENST00000567109.6	c.781+11467A>G		intron_variant		1	NM_001257.5	P1

Frequencies

GnomAD3 genomes AF: 0.0866 AC: 13160 AN: 152048 Hom.: 795 Cov.: 31

Gnomad AFR AF: 0.0211

Gnomad AMI AF: 0.138

Gnomad AMR AF: 0.0668

Gnomad ASJ AF: 0.0622

Gnomad EAS AF: 0.000963

Gnomad SAS AF: 0.0543

Gnomad FIN AF: 0.146

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.131

Gnomad OTH AF: 0.0796

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

GnomAD4 genome AF: 0.0865 AC: 13158 AN: 152166 Hom.: 796 Cov.: 31 AF XY: 0.0857 AC XY: 6377 AN XY: 74380

Gnomad4 AFR AF: 0.0211

Gnomad4 AMR AF: 0.0667

Gnomad4 ASJ AF: 0.0622

Gnomad4 EAS AF: 0.000965

Gnomad4 SAS AF: 0.0541

Gnomad4 FIN AF: 0.146

Gnomad4 NFE AF: 0.131

Gnomad4 OTH AF: 0.0792

Alfa AF: 0.107 Hom.: 139

Bravo AF: 0.0775

Asia WGS AF: 0.0220 AC: 76 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.5
DANN	Benign	0.79

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

Other links and lift over

dbSNP: rs17284098; hg19: chr16-83390078;