NM_001257.5:c.157+57010G>C

Variant names:

• chr16-82915483-G-C
• rs17675094
• NM_001257.5:c.157+57010G>C

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+57010G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.4 in 152,052 control chromosomes in the GnomAD database, including 16,013 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 0.40 (16013 hom., cov: 32)
• Consequence: CDH13 NM_001257.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.67
• Publications: 5 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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.26).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.599 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+57010G>C		intron	N/A	NP_001248.1	P55290-1
	CDH13	NM_001220488.2		c.298+57010G>C		intron	N/A	NP_001207417.1	P55290-4
	CDH13	NM_001220489.2		c.157+57010G>C		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+57010G>C		intron	N/A	ENSP00000479395.1	P55290-1
	CDH13	ENST00000431540.7	TSL:1	c.157+57010G>C		intron	N/A	ENSP00000408632.3	P55290-2
	CDH13	ENST00000268613.14	TSL:2	c.298+57010G>C		intron	N/A	ENSP00000268613.10	P55290-4

Frequencies

GnomAD3 genomes AF: 0.400 AC: 60832 AN: 151932 Hom.: 16013 Cov.: 32

Gnomad AFR AF: 0.108

Gnomad AMI AF: 0.592

Gnomad AMR AF: 0.337

Gnomad ASJ AF: 0.511

Gnomad EAS AF: 0.0414

Gnomad SAS AF: 0.311

Gnomad FIN AF: 0.489

Gnomad MID AF: 0.420

Gnomad NFE AF: 0.604

Gnomad OTH AF: 0.425

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

GnomAD4 genome AF: 0.400 AC: 60829 AN: 152052 Hom.: 16013 Cov.: 32 AF XY: 0.389 AC XY: 28939 AN XY: 74330

African (AFR) AF: 0.108 AC: 4474 AN: 41494

American (AMR) AF: 0.336 AC: 5137 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.511 AC: 1770 AN: 3466

East Asian (EAS) AF: 0.0415 AC: 215 AN: 5176

South Asian (SAS) AF: 0.311 AC: 1497 AN: 4810

European-Finnish (FIN) AF: 0.489 AC: 5157 AN: 10554

Middle Eastern (MID) AF: 0.429 AC: 126 AN: 294

European-Non Finnish (NFE) AF: 0.604 AC: 41022 AN: 67966

Other (OTH) AF: 0.424 AC: 892 AN: 2102

Alfa AF: 0.483 Hom.: 2464

Bravo AF: 0.374

Asia WGS AF: 0.189 AC: 659 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	0.64
PhyloP100		2.7
Mutation Taster		=99/1	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: rs17675094; hg19: chr16-82949088;