16-83031798-T-C

Position:

• chr16-83031798-T-C

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_001257.5(CDH13):​c.158-212T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.254 in 152,064 control chromosomes in the GnomAD database, including 5,160 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.25 (5160 hom., cov: 31)
• Consequence: CDH13 NM_001257.5 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.267

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 -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BP6: Variant 16-83031798-T-C is Benign according to our data. Variant chr16-83031798-T-C is described in ClinVar as [Benign]. Clinvar id is 1273573.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.29 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CDH13	NM_001257.5	c.158-212T>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.158-212T>C		intron_variant		1	NM_001257.5	ENSP00000479395.1

Frequencies

GnomAD3 genomes AF: 0.254 AC: 38631 AN: 151946 Hom.: 5152 Cov.: 31

Gnomad AFR AF: 0.177

Gnomad AMI AF: 0.377

Gnomad AMR AF: 0.273

Gnomad ASJ AF: 0.171

Gnomad EAS AF: 0.275

Gnomad SAS AF: 0.256

Gnomad FIN AF: 0.286

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.294

Gnomad OTH AF: 0.235

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

GnomAD4 genome AF: 0.254 AC: 38678 AN: 152064 Hom.: 5160 Cov.: 31 AF XY: 0.255 AC XY: 18951 AN XY: 74318

Gnomad4 AFR AF: 0.177

Gnomad4 AMR AF: 0.274

Gnomad4 ASJ AF: 0.171

Gnomad4 EAS AF: 0.275

Gnomad4 SAS AF: 0.257

Gnomad4 FIN AF: 0.286

Gnomad4 NFE AF: 0.294

Gnomad4 OTH AF: 0.236

Alfa AF: 0.258 Hom.: 3036

Bravo AF: 0.248

Asia WGS AF: 0.252 AC: 875 AN: 3476

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 18, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.75
DANN	Benign	0.60

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: rs9888896; hg19: chr16-83065403;