chr16-82639464-A-G
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The NM_001257.5(CDH13):c.45+12327A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000735 in 1,530,588 control chromosomes in the GnomAD database, including 6 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0037 ( 1 hom., cov: 33)
Exomes 𝑓: 0.00040 ( 5 hom. )
Consequence
CDH13
NM_001257.5 intron
NM_001257.5 intron
Scores
16
Splicing: ADA: 0.0001302
2
Clinical Significance
Conservation
PhyloP100: -0.563
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 Likely_benign. Variant got -6 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.005779505).
BP6
?
Variant 16-82639464-A-G is Benign according to our data. Variant chr16-82639464-A-G is described in ClinVar as [Benign]. Clinvar id is 3048874.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CDH13 | NM_001257.5 | c.45+12327A>G | intron_variant | ENST00000567109.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CDH13 | ENST00000567109.6 | c.45+12327A>G | intron_variant | 1 | NM_001257.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00373 AC: 568AN: 152204Hom.: 1 Cov.: 33
GnomAD3 genomes
?
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GnomAD3 exomes AF: 0.000896 AC: 115AN: 128370Hom.: 0 AF XY: 0.000839 AC XY: 59AN XY: 70286
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GnomAD4 exome AF: 0.000403 AC: 556AN: 1378266Hom.: 5 Cov.: 27 AF XY: 0.000344 AC XY: 234AN XY: 680448
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GnomAD4 genome ? AF: 0.00374 AC: 569AN: 152322Hom.: 1 Cov.: 33 AF XY: 0.00340 AC XY: 253AN XY: 74492
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
CDH13-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jun 05, 2020 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T
M_CAP
Benign
T
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationTaster
Benign
N;N;N;N;N;N;N
PrimateAI
Benign
T
PROVEAN
Benign
N
REVEL
Benign
Sift
Benign
D
Sift4G
Benign
T
Vest4
MVP
MPC
ClinPred
T
GERP RS
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
dbscSNV1_ADA
Benign
dbscSNV1_RF
Benign
SpliceAI score (max)
Details are displayed if max score is > 0.2
DS_DL_spliceai
Position offset: 1
Find out detailed SpliceAI scores and Pangolin per-transcript scores at