chr16-83105719-A-G

Variant names:

• chr16-83105719-A-G
• rs9941339
• NM_001257.5:c.367-19666A>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.367-19666A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.571 in 152,074 control chromosomes in the GnomAD database, including 25,103 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 0.57 (25103 hom., cov: 33)
• Consequence: CDH13 NM_001257.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.348
• Publications: 5 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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.604 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CDH13	NM_001257.5	c.367-19666A>G		intron_variant	Intron 3 of 13	ENST00000567109.6	NP_001248.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CDH13	ENST00000567109.6	c.367-19666A>G		intron_variant	Intron 3 of 13	1	NM_001257.5	ENSP00000479395.1

Frequencies

GnomAD3 genomes AF: 0.571 AC: 86766 AN: 151956 Hom.: 25088 Cov.: 33

Gnomad AFR AF: 0.552

Gnomad AMI AF: 0.601

Gnomad AMR AF: 0.522

Gnomad ASJ AF: 0.621

Gnomad EAS AF: 0.384

Gnomad SAS AF: 0.452

Gnomad FIN AF: 0.595

Gnomad MID AF: 0.682

Gnomad NFE AF: 0.609

Gnomad OTH AF: 0.590

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

GnomAD4 genome AF: 0.571 AC: 86824 AN: 152074 Hom.: 25103 Cov.: 33 AF XY: 0.568 AC XY: 42214 AN XY: 74350

African (AFR) AF: 0.551 AC: 22859 AN: 41454

American (AMR) AF: 0.521 AC: 7964 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.621 AC: 2156 AN: 3472

East Asian (EAS) AF: 0.385 AC: 1990 AN: 5170

South Asian (SAS) AF: 0.454 AC: 2190 AN: 4826

European-Finnish (FIN) AF: 0.595 AC: 6289 AN: 10572

Middle Eastern (MID) AF: 0.688 AC: 201 AN: 292

European-Non Finnish (NFE) AF: 0.609 AC: 41385 AN: 67972

Other (OTH) AF: 0.588 AC: 1243 AN: 2114

Alfa AF: 0.599 Hom.: 42295

Bravo AF: 0.565

Asia WGS AF: 0.450 AC: 1566 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	4.2
DANN	Benign	0.41
PhyloP100		0.35
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: rs9941339; hg19: chr16-83139324;