rs9319578

Variant names:

• chr16-82902438-A-G
• rs9319578
• NM_001257.5:c.157+43965A>G

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_001257.5(CDH13):​c.157+43965A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.931 in 152,008 control chromosomes in the GnomAD database, including 65,986 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 0.93 (65986 hom., cov: 29)
• Consequence: CDH13 NM_001257.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.35
• Publications: 2 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]

LOC124903733 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.26).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.976 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CDH13	NM_001257.5	MANE Select	c.157+43965A>G		intron	N/A	NP_001248.1	P55290-1
	CDH13	NM_001220488.2		c.298+43965A>G		intron	N/A	NP_001207417.1	P55290-4
	CDH13	NM_001220489.2		c.157+43965A>G		intron	N/A	NP_001207418.1	P55290-5

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CDH13	ENST00000567109.6	TSL:1 MANE Select	c.157+43965A>G		intron	N/A	ENSP00000479395.1	P55290-1
	CDH13	ENST00000431540.7	TSL:1	c.157+43965A>G		intron	N/A	ENSP00000408632.3	P55290-2
	CDH13	ENST00000268613.14	TSL:2	c.298+43965A>G		intron	N/A	ENSP00000268613.10	P55290-4

Frequencies

GnomAD3 genomes AF: 0.931 AC: 141382 AN: 151890 Hom.: 65928 Cov.: 29

Gnomad AFR AF: 0.984

Gnomad AMI AF: 0.966

Gnomad AMR AF: 0.939

Gnomad ASJ AF: 0.923

Gnomad EAS AF: 0.871

Gnomad SAS AF: 0.906

Gnomad FIN AF: 0.834

Gnomad MID AF: 0.869

Gnomad NFE AF: 0.918

Gnomad OTH AF: 0.927

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

GnomAD4 genome AF: 0.931 AC: 141501 AN: 152008 Hom.: 65986 Cov.: 29 AF XY: 0.926 AC XY: 68775 AN XY: 74278

African (AFR) AF: 0.984 AC: 40844 AN: 41508

American (AMR) AF: 0.939 AC: 14349 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.923 AC: 3204 AN: 3472

East Asian (EAS) AF: 0.870 AC: 4472 AN: 5140

South Asian (SAS) AF: 0.906 AC: 4355 AN: 4808

European-Finnish (FIN) AF: 0.834 AC: 8751 AN: 10494

Middle Eastern (MID) AF: 0.877 AC: 256 AN: 292

European-Non Finnish (NFE) AF: 0.918 AC: 62439 AN: 67994

Other (OTH) AF: 0.929 AC: 1950 AN: 2100

Alfa AF: 0.925 Hom.: 31464

Bravo AF: 0.942

Asia WGS AF: 0.871 AC: 3030 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.26
CADD	Benign	20
DANN	Benign	0.79
PhyloP100		2.3
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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs9319578;

hg19: chr16-82936043;