16-82982045-A-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001257.5(CDH13):​c.158-49965A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.43 in 151,996 control chromosomes in the GnomAD database, including 14,338 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 0.43 ( 14338 hom., cov: 32)

Consequence

CDH13
NM_001257.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.81
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.95).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.483 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
CDH13NM_001257.5 linkuse as main transcriptc.158-49965A>C intron_variant ENST00000567109.6 NP_001248.1
LOC101928417NR_110937.1 linkuse as main transcriptn.173+8081T>G intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
CDH13ENST00000567109.6 linkuse as main transcriptc.158-49965A>C intron_variant 1 NM_001257.5 ENSP00000479395 P1P55290-1
ENST00000565238.1 linkuse as main transcriptn.173+8081T>G intron_variant, non_coding_transcript_variant 1

Frequencies

GnomAD3 genomes
AF:
0.430
AC:
65285
AN:
151878
Hom.:
14303
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.362
Gnomad AMI
AF:
0.528
Gnomad AMR
AF:
0.492
Gnomad ASJ
AF:
0.293
Gnomad EAS
AF:
0.456
Gnomad SAS
AF:
0.475
Gnomad FIN
AF:
0.564
Gnomad MID
AF:
0.380
Gnomad NFE
AF:
0.438
Gnomad OTH
AF:
0.407
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.430
AC:
65364
AN:
151996
Hom.:
14338
Cov.:
32
AF XY:
0.437
AC XY:
32478
AN XY:
74290
show subpopulations
Gnomad4 AFR
AF:
0.363
Gnomad4 AMR
AF:
0.492
Gnomad4 ASJ
AF:
0.293
Gnomad4 EAS
AF:
0.456
Gnomad4 SAS
AF:
0.475
Gnomad4 FIN
AF:
0.564
Gnomad4 NFE
AF:
0.438
Gnomad4 OTH
AF:
0.413
Alfa
AF:
0.413
Hom.:
7396
Bravo
AF:
0.421
Asia WGS
AF:
0.434
AC:
1510
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.95
CADD
Benign
0.0060
DANN
Benign
0.62

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs4782742; hg19: chr16-83015650; API