rs11150556

Variant names:

• chr16-83236936-T-C
• rs11150556
• NM_001257.5:c.636+19439T>C

Your query was ambiguous. Multiple possible variants found:

• chr16-83236936-T-C
• chr16-83236936-T-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.636+19439T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.527 in 151,604 control chromosomes in the GnomAD database, including 21,505 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 0.53 (21505 hom., cov: 30)
• Consequence: CDH13 NM_001257.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.306
• Publications: 11 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.842 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CDH13	NM_001257.5	c.636+19439T>C		intron_variant	Intron 5 of 13	ENST00000567109.6	NP_001248.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CDH13	ENST00000567109.6	c.636+19439T>C		intron_variant	Intron 5 of 13	1	NM_001257.5	ENSP00000479395.1

Frequencies

GnomAD3 genomes AF: 0.527 AC: 79847 AN: 151484 Hom.: 21494 Cov.: 30

Gnomad AFR AF: 0.510

Gnomad AMI AF: 0.508

Gnomad AMR AF: 0.616

Gnomad ASJ AF: 0.484

Gnomad EAS AF: 0.863

Gnomad SAS AF: 0.641

Gnomad FIN AF: 0.448

Gnomad MID AF: 0.510

Gnomad NFE AF: 0.498

Gnomad OTH AF: 0.545

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

GnomAD4 genome AF: 0.527 AC: 79903 AN: 151604 Hom.: 21505 Cov.: 30 AF XY: 0.530 AC XY: 39245 AN XY: 74016

African (AFR) AF: 0.510 AC: 21058 AN: 41312

American (AMR) AF: 0.617 AC: 9396 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.484 AC: 1681 AN: 3470

East Asian (EAS) AF: 0.863 AC: 4395 AN: 5092

South Asian (SAS) AF: 0.642 AC: 3083 AN: 4800

European-Finnish (FIN) AF: 0.448 AC: 4695 AN: 10482

Middle Eastern (MID) AF: 0.507 AC: 148 AN: 292

European-Non Finnish (NFE) AF: 0.498 AC: 33830 AN: 67896

Other (OTH) AF: 0.547 AC: 1154 AN: 2108

Alfa AF: 0.517 Hom.: 31381

Bravo AF: 0.541

Asia WGS AF: 0.704 AC: 2446 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.3
DANN	Benign	0.75
PhyloP100		0.31
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: rs11150556; hg19: chr16-83270541;