chr16-82915483-G-C

Position:

• chr16-82915483-G-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_001257.5(CDH13):​c.157+57010G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.4 in 152,052 control chromosomes in the GnomAD database, including 16,013 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 0.40 (16013 hom., cov: 32)
• Consequence: CDH13 NM_001257.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.67

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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.26).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.599 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CDH13	NM_001257.5	c.157+57010G>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.157+57010G>C		intron_variant		1	NM_001257.5	ENSP00000479395.1

Frequencies

GnomAD3 genomes AF: 0.400 AC: 60832 AN: 151932 Hom.: 16013 Cov.: 32

Gnomad AFR AF: 0.108

Gnomad AMI AF: 0.592

Gnomad AMR AF: 0.337

Gnomad ASJ AF: 0.511

Gnomad EAS AF: 0.0414

Gnomad SAS AF: 0.311

Gnomad FIN AF: 0.489

Gnomad MID AF: 0.420

Gnomad NFE AF: 0.604

Gnomad OTH AF: 0.425

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

GnomAD4 genome AF: 0.400 AC: 60829 AN: 152052 Hom.: 16013 Cov.: 32 AF XY: 0.389 AC XY: 28939 AN XY: 74330

Gnomad4 AFR AF: 0.108

Gnomad4 AMR AF: 0.336

Gnomad4 ASJ AF: 0.511

Gnomad4 EAS AF: 0.0415

Gnomad4 SAS AF: 0.311

Gnomad4 FIN AF: 0.489

Gnomad4 NFE AF: 0.604

Gnomad4 OTH AF: 0.424

Alfa AF: 0.483 Hom.: 2464

Bravo AF: 0.374

Asia WGS AF: 0.189 AC: 659 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.26
CADD	Benign	20
DANN	Benign	0.64

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: rs17675094; hg19: chr16-82949088;