NM_001257.5:c.636+19147G>A

Variant names:

• chr16-83236644-G-A
• rs11150555
• NM_001257.5:c.636+19147G>A

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+19147G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.712 in 151,862 control chromosomes in the GnomAD database, including 39,801 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 0.71 (39801 hom., cov: 31)
• Consequence: CDH13 NM_001257.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0320
• Publications: 3 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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.92 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CDH13	NM_001257.5	c.636+19147G>A		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+19147G>A		intron_variant	Intron 5 of 13	1	NM_001257.5	ENSP00000479395.1

Frequencies

GnomAD3 genomes AF: 0.712 AC: 107976 AN: 151744 Hom.: 39766 Cov.: 31

Gnomad AFR AF: 0.504

Gnomad AMI AF: 0.829

Gnomad AMR AF: 0.800

Gnomad ASJ AF: 0.759

Gnomad EAS AF: 0.942

Gnomad SAS AF: 0.846

Gnomad FIN AF: 0.805

Gnomad MID AF: 0.756

Gnomad NFE AF: 0.772

Gnomad OTH AF: 0.731

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

GnomAD4 genome AF: 0.712 AC: 108055 AN: 151862 Hom.: 39801 Cov.: 31 AF XY: 0.718 AC XY: 53233 AN XY: 74176

African (AFR) AF: 0.504 AC: 20837 AN: 41354

American (AMR) AF: 0.800 AC: 12215 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.759 AC: 2631 AN: 3468

East Asian (EAS) AF: 0.942 AC: 4842 AN: 5140

South Asian (SAS) AF: 0.847 AC: 4081 AN: 4820

European-Finnish (FIN) AF: 0.805 AC: 8471 AN: 10526

Middle Eastern (MID) AF: 0.755 AC: 219 AN: 290

European-Non Finnish (NFE) AF: 0.772 AC: 52458 AN: 67982

Other (OTH) AF: 0.732 AC: 1545 AN: 2110

Alfa AF: 0.754 Hom.: 90578

Bravo AF: 0.702

Asia WGS AF: 0.863 AC: 2997 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.48
DANN	Benign	0.22
PhyloP100		-0.032
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: rs11150555; hg19: chr16-83270249;