chr7-106012942-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_152750.5(CDHR3):c.1135C>T(p.Pro379Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000568 in 1,613,700 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (no stars).
Frequency
Genomes: 𝑓 0.00099 ( 1 hom., cov: 32)
Exomes 𝑓: 0.00052 ( 3 hom. )
Consequence
CDHR3
NM_152750.5 missense
NM_152750.5 missense
Scores
5
13
Clinical Significance
Conservation
PhyloP100: 3.52
Genes affected
CDHR3 (HGNC:26308): (cadherin related family member 3) Predicted to enable cadherin binding activity and calcium ion binding activity. Predicted to be involved in calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules; cell morphogenesis; and cell-cell junction organization. Located in plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.009130985).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CDHR3 | NM_152750.5 | c.1135C>T | p.Pro379Ser | missense_variant | 9/19 | ENST00000317716.14 | |
CDHR3 | NM_001301161.2 | c.871C>T | p.Pro291Ser | missense_variant | 8/18 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CDHR3 | ENST00000317716.14 | c.1135C>T | p.Pro379Ser | missense_variant | 9/19 | 1 | NM_152750.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000986 AC: 150AN: 152138Hom.: 1 Cov.: 32
GnomAD3 genomes
?
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GnomAD3 exomes AF: 0.00106 AC: 263AN: 248984Hom.: 1 AF XY: 0.00109 AC XY: 147AN XY: 135074
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GnomAD4 exome AF: 0.000525 AC: 767AN: 1461444Hom.: 3 Cov.: 31 AF XY: 0.000527 AC XY: 383AN XY: 727034
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GnomAD4 genome ? AF: 0.000985 AC: 150AN: 152256Hom.: 1 Cov.: 32 AF XY: 0.00165 AC XY: 123AN XY: 74448
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Susceptibility to nonsyndromic otitis media Uncertain:1
Uncertain significance, no assertion criteria provided | research | Santos-Cortez Lab, University of Colorado School of Medicine | Feb 01, 2013 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Uncertain
DEOGEN2
Benign
T;T;.
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Benign
D
LIST_S2
Benign
T;T;T
MetaRNN
Benign
T;T;T
MetaSVM
Benign
T
MutationAssessor
Uncertain
M;.;.
MutationTaster
Benign
D;D;D;D;D
PrimateAI
Benign
T
PROVEAN
Uncertain
D;D;D
REVEL
Benign
Sift
Benign
T;T;T
Sift4G
Benign
T;T;D
Polyphen
D;.;.
Vest4
MVP
MPC
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