Genetic Variant CDH13:c.157+53473G>C (chr16-82911946-G-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001257.5(CDH13):c.157+53473G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.76 in 151,574 control chromosomes in the GnomAD database, including 43,826 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 0.76 ( 43826 hom., cov: 29)

Consequence

CDH13
NM_001257.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.810

Publications

3 publications found

Variant links:

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]

CDH13 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.91).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.819 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

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
CDH13	NM_001257.5	MANE Select	c.157+53473G>C	intron	N/A	NP_001248.1	P55290-1
CDH13	NM_001220488.2		c.298+53473G>C	intron	N/A	NP_001207417.1	P55290-4
CDH13	NM_001220489.2		c.157+53473G>C	intron	N/A	NP_001207418.1	P55290-5

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
CDH13	ENST00000567109.6	TSL:1 MANE Select	c.157+53473G>C	intron	N/A	ENSP00000479395.1	P55290-1
CDH13	ENST00000431540.7	TSL:1	c.157+53473G>C	intron	N/A	ENSP00000408632.3	P55290-2
CDH13	ENST00000268613.14	TSL:2	c.298+53473G>C	intron	N/A	ENSP00000268613.10	P55290-4

Frequencies

GnomAD3 genomes

AF:

0.760

AC:

115136

AN:

151458

Hom.:

43794

Cov.:

show subpopulations

Gnomad AFR

AF:

0.722

Gnomad AMI

AF:

0.791

Gnomad AMR

AF:

0.758

Gnomad ASJ

AF:

0.803

Gnomad EAS

AF:

0.834

Gnomad SAS

AF:

0.842

Gnomad FIN

AF:

0.761

Gnomad MID

AF:

0.742

Gnomad NFE

AF:

0.770

Gnomad OTH

AF:

0.756

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

GnomAD4 genome

AF:

0.760

AC:

115221

AN:

151574

Hom.:

43826

Cov.:

AF XY:

0.761

AC XY:

56349

AN XY:

74006

show subpopulations

African (AFR)

AF:

0.723

AC:

29833

AN:

41288

American (AMR)

AF:

0.758

AC:

11551

AN:

15244

Ashkenazi Jewish (ASJ)

AF:

0.803

AC:

2787

AN:

3472

East Asian (EAS)

AF:

0.833

AC:

4183

AN:

5024

South Asian (SAS)

AF:

0.841

AC:

4035

AN:

4798

European-Finnish (FIN)

AF:

0.761

AC:

7981

AN:

10494

Middle Eastern (MID)

AF:

0.747

AC:

218

AN:

292

European-Non Finnish (NFE)

AF:

0.770

AC:

52312

AN:

67942

Other (OTH)

AF:

0.759

AC:

1601

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

1358

2716

4073

5431

6789

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

858

1716

2574

3432

4290

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.760

Hom.:

5444

Bravo

AF:

0.758

Asia WGS

AF:

0.810

AC:

2817

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.61

(source)

DANN

Benign

0.74

PhyloP100

-0.81

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over