NM_001257.5:c.45+60682A>G

Variant names:

• chr16-82687819-A-G
• rs11640875
• NM_001257.5:c.45+60682A>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.45+60682A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.556 in 151,896 control chromosomes in the GnomAD database, including 24,782 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 0.56 (24782 hom., cov: 30)
• Consequence: CDH13 NM_001257.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.463
• Publications: 14 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 (NFE) allele frequency at 95% confidence interval = 0.652 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.45+60682A>G		intron	N/A	NP_001248.1
	CDH13	NM_001220488.2		c.186+48354A>G		intron	N/A	NP_001207417.1
	CDH13	NM_001220489.2		c.45+60682A>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.45+60682A>G		intron	N/A	ENSP00000479395.1
	CDH13	ENST00000431540.7	TSL:1	c.45+60682A>G		intron	N/A	ENSP00000408632.3
	CDH13	ENST00000567445.1	TSL:1	c.45+60682A>G		intron	N/A	ENSP00000456297.1

Frequencies

GnomAD3 genomes AF: 0.557 AC: 84477 AN: 151778 Hom.: 24771 Cov.: 30

Gnomad AFR AF: 0.405

Gnomad AMI AF: 0.582

Gnomad AMR AF: 0.446

Gnomad ASJ AF: 0.550

Gnomad EAS AF: 0.429

Gnomad SAS AF: 0.592

Gnomad FIN AF: 0.712

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.657

Gnomad OTH AF: 0.542

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

GnomAD4 genome AF: 0.556 AC: 84515 AN: 151896 Hom.: 24782 Cov.: 30 AF XY: 0.559 AC XY: 41467 AN XY: 74242

African (AFR) AF: 0.405 AC: 16783 AN: 41410

American (AMR) AF: 0.446 AC: 6810 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.550 AC: 1907 AN: 3466

East Asian (EAS) AF: 0.428 AC: 2201 AN: 5144

South Asian (SAS) AF: 0.593 AC: 2841 AN: 4792

European-Finnish (FIN) AF: 0.712 AC: 7526 AN: 10570

Middle Eastern (MID) AF: 0.463 AC: 136 AN: 294

European-Non Finnish (NFE) AF: 0.657 AC: 44629 AN: 67918

Other (OTH) AF: 0.545 AC: 1152 AN: 2112

Alfa AF: 0.608 Hom.: 96909

Bravo AF: 0.525

Asia WGS AF: 0.506 AC: 1757 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.47
DANN	Benign	0.35
PhyloP100		-0.46
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: rs11640875; hg19: chr16-82721424; COSMIC: COSV51872104; COSMIC: COSV51872104;