rs11861609

Variant names:

• chr16-83351061-C-G
• rs11861609
• NM_001257.5:c.781+6055C>G

Your query was ambiguous. Multiple possible variants found:

• chr16-83351061-C-G
• chr16-83351061-C-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.781+6055C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.453 in 152,012 control chromosomes in the GnomAD database, including 17,015 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 0.45 (17015 hom., cov: 32)
• Consequence: CDH13 NM_001257.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.276
• Publications: 4 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=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.656 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.781+6055C>G		intron	N/A	NP_001248.1
	CDH13	NM_001220488.2		c.922+6055C>G		intron	N/A	NP_001207417.1
	CDH13	NM_001220489.2		c.664+6055C>G		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.781+6055C>G		intron	N/A	ENSP00000479395.1
	CDH13	ENST00000268613.14	TSL:2	c.922+6055C>G		intron	N/A	ENSP00000268613.10
	CDH13	ENST00000428848.7	TSL:2	c.664+6055C>G		intron	N/A	ENSP00000394557.3

Frequencies

GnomAD3 genomes AF: 0.453 AC: 68851 AN: 151894 Hom.: 16995 Cov.: 32

Gnomad AFR AF: 0.662

Gnomad AMI AF: 0.341

Gnomad AMR AF: 0.368

Gnomad ASJ AF: 0.403

Gnomad EAS AF: 0.180

Gnomad SAS AF: 0.333

Gnomad FIN AF: 0.358

Gnomad MID AF: 0.541

Gnomad NFE AF: 0.393

Gnomad OTH AF: 0.456

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

GnomAD4 genome AF: 0.453 AC: 68912 AN: 152012 Hom.: 17015 Cov.: 32 AF XY: 0.446 AC XY: 33133 AN XY: 74292

African (AFR) AF: 0.662 AC: 27440 AN: 41446

American (AMR) AF: 0.368 AC: 5621 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.403 AC: 1398 AN: 3466

East Asian (EAS) AF: 0.180 AC: 931 AN: 5174

South Asian (SAS) AF: 0.332 AC: 1599 AN: 4818

European-Finnish (FIN) AF: 0.358 AC: 3777 AN: 10564

Middle Eastern (MID) AF: 0.548 AC: 160 AN: 292

European-Non Finnish (NFE) AF: 0.393 AC: 26714 AN: 67950

Other (OTH) AF: 0.455 AC: 961 AN: 2112

Alfa AF: 0.268 Hom.: 562

Bravo AF: 0.464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.5
DANN	Benign	0.54
PhyloP100		0.28
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: rs11861609; hg19: chr16-83384666;