chr20-61852801-C-T
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Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2
The NM_001794.5(CDH4):c.780C>T(p.Pro260=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000254 in 1,614,088 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 (★).
Frequency
Genomes: 𝑓 0.000020 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000026 ( 0 hom. )
Consequence
CDH4
NM_001794.5 synonymous
NM_001794.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.187
Genes affected
CDH4 (HGNC:1763): (cadherin 4) This gene is a classical cadherin from the cadherin superfamily. The encoded protein is a calcium-dependent cell-cell adhesion glycoprotein comprised of five extracellular cadherin repeats, a transmembrane region and a highly conserved cytoplasmic tail. Based on studies in chicken and mouse, this cadherin is thought to play an important role during brain segmentation and neuronal outgrowth. In addition, a role in kidney and muscle development is indicated. Of particular interest are studies showing stable cis-heterodimers of cadherins 2 and 4 in cotransfected cell lines. Previously thought to interact in an exclusively homophilic manner, this is the first evidence of cadherin heterodimerization. Three transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Nov 2011]
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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 (BayesDel_noAF=-0.39).
BP6
Variant 20-61852801-C-T is Benign according to our data. Variant chr20-61852801-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 751029.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=0.187 with no splicing effect.
BS2
High AC in GnomAdExome4 at 38 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CDH4 | NM_001794.5 | c.780C>T | p.Pro260= | synonymous_variant | 6/16 | ENST00000614565.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CDH4 | ENST00000614565.5 | c.780C>T | p.Pro260= | synonymous_variant | 6/16 | 1 | NM_001794.5 | P1 | |
CDH4 | ENST00000543233.2 | c.558C>T | p.Pro186= | synonymous_variant | 5/15 | 2 | |||
CDH4 | ENST00000611855.4 | c.498C>T | p.Pro166= | synonymous_variant | 5/15 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152258Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.0000636 AC: 16AN: 251378Hom.: 0 AF XY: 0.0000662 AC XY: 9AN XY: 135876
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GnomAD4 exome AF: 0.0000260 AC: 38AN: 1461712Hom.: 0 Cov.: 31 AF XY: 0.0000234 AC XY: 17AN XY: 727158
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GnomAD4 genome AF: 0.0000197 AC: 3AN: 152376Hom.: 0 Cov.: 33 AF XY: 0.0000268 AC XY: 2AN XY: 74512
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Sep 13, 2018 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at