16-82792902-C-G

Variant names:

• chr16-82792902-C-G
• rs17192646
• NM_001257.5:c.46-65460C>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0300
• Publications: 2 publications found

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]

ENSG00000260862 (HGNC:):

ACMG classification

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
CDH13	NM_001257.5	c.46-65460C>G		intron_variant	Intron 1 of 13	ENST00000567109.6	NP_001248.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CDH13	ENST00000567109.6	c.46-65460C>G		intron_variant	Intron 1 of 13	1	NM_001257.5	ENSP00000479395.1

Frequencies

GnomAD3 genomes AF: 0.0690 AC: 10252 AN: 148564 Hom.: 438 Cov.: 34

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

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

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

Other links and lift over

dbSNP: rs17192646; hg19: chr16-82826507;