16-83043029-G-T

Variant names:

• chr16-83043029-G-T
• rs4783307
• NM_001257.5:c.366+10811G>T

Variant summary

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

The ENST00000567109.6(CDH13):​c.366+10811G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.463 in 152,006 control chromosomes in the GnomAD database, including 16,951 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 0.46 (16951 hom., cov: 33)
• Consequence: CDH13 ENST00000567109.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.25
• Publications: 7 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=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.585 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000567109.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CDH13	NM_001257.5	MANE Select	c.366+10811G>T		intron	N/A	NP_001248.1
	CDH13	NM_001220488.2		c.507+10811G>T		intron	N/A	NP_001207417.1
	CDH13	NM_001220489.2		c.366+10811G>T		intron	N/A	NP_001207418.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CDH13	ENST00000567109.6	TSL:1 MANE Select	c.366+10811G>T		intron	N/A	ENSP00000479395.1
	CDH13	ENST00000431540.7	TSL:1	c.366+10811G>T		intron	N/A	ENSP00000408632.3
	CDH13	ENST00000268613.14	TSL:2	c.507+10811G>T		intron	N/A	ENSP00000268613.10

Frequencies

GnomAD3 genomes AF: 0.463 AC: 70334 AN: 151888 Hom.: 16914 Cov.: 33

Gnomad AFR AF: 0.590

Gnomad AMI AF: 0.448

Gnomad AMR AF: 0.433

Gnomad ASJ AF: 0.532

Gnomad EAS AF: 0.483

Gnomad SAS AF: 0.428

Gnomad FIN AF: 0.313

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.412

Gnomad OTH AF: 0.491

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

GnomAD4 genome AF: 0.463 AC: 70415 AN: 152006 Hom.: 16951 Cov.: 33 AF XY: 0.456 AC XY: 33850 AN XY: 74280

African (AFR) AF: 0.591 AC: 24481 AN: 41428

American (AMR) AF: 0.433 AC: 6612 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.532 AC: 1843 AN: 3466

East Asian (EAS) AF: 0.483 AC: 2494 AN: 5166

South Asian (SAS) AF: 0.428 AC: 2063 AN: 4824

European-Finnish (FIN) AF: 0.313 AC: 3305 AN: 10562

Middle Eastern (MID) AF: 0.483 AC: 142 AN: 294

European-Non Finnish (NFE) AF: 0.412 AC: 28035 AN: 67974

Other (OTH) AF: 0.488 AC: 1032 AN: 2114

Alfa AF: 0.445 Hom.: 22193

Bravo AF: 0.479

Asia WGS AF: 0.481 AC: 1672 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	16
DANN	Benign	0.62
PhyloP100		1.2
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: rs4783307; hg19: chr16-83076634;