chr16-83031886-G-C

Position:

• chr16-83031886-G-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.158-124G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.105 in 742,346 control chromosomes in the GnomAD database, including 4,387 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.12 (1144 hom., cov: 32)
  • Exomes 𝑓: 0.10 (3243 hom.)
• Consequence: CDH13 NM_001257.5 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.05

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 -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BP6: Variant 16-83031886-G-C is Benign according to our data. Variant chr16-83031886-G-C is described in ClinVar as [Benign]. Clinvar id is 1239670.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.164 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CDH13	NM_001257.5	c.158-124G>C		intron_variant		ENST00000567109.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CDH13	ENST00000567109.6	c.158-124G>C		intron_variant		1	NM_001257.5	P1

Frequencies

GnomAD3 genomes AF: 0.117 AC: 17845 AN: 152040 Hom.: 1143 Cov.: 32

Gnomad AFR AF: 0.167

Gnomad AMI AF: 0.149

Gnomad AMR AF: 0.0787

Gnomad ASJ AF: 0.114

Gnomad EAS AF: 0.0521

Gnomad SAS AF: 0.108

Gnomad FIN AF: 0.116

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.102

Gnomad OTH AF: 0.109

GnomAD4 exome AF: 0.102 AC: 60032 AN: 590188 Hom.: 3243 AF XY: 0.102 AC XY: 31150 AN XY: 305412

Gnomad4 AFR exome AF: 0.168

Gnomad4 AMR exome AF: 0.0661

Gnomad4 ASJ exome AF: 0.115

Gnomad4 EAS exome AF: 0.0726

Gnomad4 SAS exome AF: 0.103

Gnomad4 FIN exome AF: 0.117

Gnomad4 NFE exome AF: 0.101

Gnomad4 OTH exome AF: 0.104

GnomAD4 genome AF: 0.117 AC: 17857 AN: 152158 Hom.: 1144 Cov.: 32 AF XY: 0.115 AC XY: 8589 AN XY: 74414

Gnomad4 AFR AF: 0.167

Gnomad4 AMR AF: 0.0784

Gnomad4 ASJ AF: 0.114

Gnomad4 EAS AF: 0.0526

Gnomad4 SAS AF: 0.107

Gnomad4 FIN AF: 0.116

Gnomad4 NFE AF: 0.102

Gnomad4 OTH AF: 0.110

Alfa AF: 0.0376 Hom.: 40

Bravo AF: 0.116

Asia WGS AF: 0.117 AC: 407 AN: 3478

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	-0.88
CADD	Benign	0.21
DANN	Benign	0.39

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: rs7189859; hg19: chr16-83065491;