chr16-83178793-G-T

Variant names:

• chr16-83178793-G-T
• rs8055236
• NM_001257.5:c.484-38552G>T

Variant summary

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

The NM_001257.5(CDH13):​c.484-38552G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.275 in 151,772 control chromosomes in the GnomAD database, including 7,669 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 0.28 (7669 hom., cov: 31)
• Consequence: CDH13 NM_001257.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.234
• Publications: 35 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=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.52 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001257.5. 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.484-38552G>T		intron	N/A	NP_001248.1
	CDH13	NM_001220488.2		c.625-38552G>T		intron	N/A	NP_001207417.1
	CDH13	NM_001220489.2		c.367-38552G>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.484-38552G>T		intron	N/A	ENSP00000479395.1
	CDH13	ENST00000431540.7	TSL:1	c.484-2077G>T		intron	N/A	ENSP00000408632.3
	CDH13	ENST00000268613.14	TSL:2	c.625-38552G>T		intron	N/A	ENSP00000268613.10

Frequencies

GnomAD3 genomes AF: 0.275 AC: 41697 AN: 151654 Hom.: 7643 Cov.: 31

Gnomad AFR AF: 0.526

Gnomad AMI AF: 0.425

Gnomad AMR AF: 0.160

Gnomad ASJ AF: 0.226

Gnomad EAS AF: 0.112

Gnomad SAS AF: 0.148

Gnomad FIN AF: 0.179

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.186

Gnomad OTH AF: 0.257

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

GnomAD4 genome AF: 0.275 AC: 41776 AN: 151772 Hom.: 7669 Cov.: 31 AF XY: 0.271 AC XY: 20084 AN XY: 74164

African (AFR) AF: 0.526 AC: 21763 AN: 41372

American (AMR) AF: 0.160 AC: 2432 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.226 AC: 786 AN: 3472

East Asian (EAS) AF: 0.112 AC: 576 AN: 5134

South Asian (SAS) AF: 0.149 AC: 719 AN: 4812

European-Finnish (FIN) AF: 0.179 AC: 1885 AN: 10502

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.186 AC: 12619 AN: 67944

Other (OTH) AF: 0.257 AC: 540 AN: 2104

Alfa AF: 0.208 Hom.: 16559

Bravo AF: 0.287

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.42
DANN	Benign	0.35
PhyloP100		-0.23
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: rs8055236; hg19: chr16-83212398;