rs200234049
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS1
The NM_001797.4(CDH11):c.1247C>T(p.Pro416Leu) variant causes a missense change. The variant allele was found at a frequency of 0.0000379 in 1,611,194 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars). Synonymous variant affecting the same amino acid position (i.e. P416P) has been classified as Likely benign.
Frequency
Genomes: 𝑓 0.000046 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000037 ( 0 hom. )
Consequence
CDH11
NM_001797.4 missense
NM_001797.4 missense
Scores
1
4
13
Clinical Significance
Conservation
PhyloP100: 6.46
Genes affected
CDH11 (HGNC:1750): (cadherin 11) This gene encodes a type II classical cadherin from the cadherin superfamily, integral membrane proteins that mediate calcium-dependent cell-cell adhesion. Mature cadherin proteins are composed of a large N-terminal extracellular domain, a single membrane-spanning domain, and a small, highly conserved C-terminal cytoplasmic domain. Type II (atypical) cadherins are defined based on their lack of a HAV cell adhesion recognition sequence specific to type I cadherins. Expression of this particular cadherin in osteoblastic cell lines, and its upregulation during differentiation, suggests a specific function in bone development and maintenance. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -9 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.0229325).
BP6
?
Variant 16-64982054-G-A is Benign according to our data. Variant chr16-64982054-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 254107.Status of the report is no_assertion_criteria_provided, 0 stars.
BS1
?
Variant frequency is greater than expected in population amr. gnomad4 allele frequency = 0.000046 (7/152048) while in subpopulation AMR AF= 0.000458 (7/15276). AF 95% confidence interval is 0.000215. There are 0 homozygotes in gnomad4. There are 4 alleles in male gnomad4 subpopulation. This position pass quality control queck.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CDH11 | NM_001797.4 | c.1247C>T | p.Pro416Leu | missense_variant | 8/13 | ENST00000268603.9 | |
CDH11 | NM_001308392.2 | c.1247C>T | p.Pro416Leu | missense_variant | 8/14 | ||
CDH11 | NM_001330576.2 | c.869C>T | p.Pro290Leu | missense_variant | 7/12 | ||
CDH11 | XM_047433486.1 | c.869C>T | p.Pro290Leu | missense_variant | 7/12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CDH11 | ENST00000268603.9 | c.1247C>T | p.Pro416Leu | missense_variant | 8/13 | 1 | NM_001797.4 | P1 | |
CDH11 | ENST00000394156.7 | c.1247C>T | p.Pro416Leu | missense_variant | 8/14 | 1 | |||
ENST00000624875.1 | n.1174C>T | non_coding_transcript_exon_variant | 1/1 | ||||||
CDH11 | ENST00000566827.5 | c.869C>T | p.Pro290Leu | missense_variant | 7/12 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000461 AC: 7AN: 151930Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000133 AC: 33AN: 248748Hom.: 0 AF XY: 0.0000893 AC XY: 12AN XY: 134330
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GnomAD4 exome AF: 0.0000370 AC: 54AN: 1459146Hom.: 0 Cov.: 31 AF XY: 0.0000317 AC XY: 23AN XY: 725666
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GnomAD4 genome ? AF: 0.0000460 AC: 7AN: 152048Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74312
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Oromandibular-limb hypogenesis spectrum Benign:1
Likely benign, no assertion criteria provided | research | CHU Sainte-Justine Research Center, University of Montreal | Aug 12, 2016 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Uncertain
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
D;D;D
M_CAP
Benign
T
MetaRNN
Benign
T;T;T
MetaSVM
Benign
T
MutationAssessor
Benign
L;L;.
MutationTaster
Benign
D;D;D
PrimateAI
Uncertain
T
PROVEAN
Uncertain
D;D;D
REVEL
Benign
Sift
Benign
T;T;T
Sift4G
Benign
T;T;T
Polyphen
P;B;.
Vest4
MVP
MPC
0.47
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at