chr20-61852870-C-T
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2
The NM_001794.5(CDH4):c.849C>T(p.Asn283=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00543 in 1,613,958 control chromosomes in the GnomAD database, including 33 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0046 ( 4 hom., cov: 33)
Exomes 𝑓: 0.0055 ( 29 hom. )
Consequence
CDH4
NM_001794.5 synonymous
NM_001794.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.00500
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=-0.32).
BP6
?
Variant 20-61852870-C-T is Benign according to our data. Variant chr20-61852870-C-T is described in ClinVar as [Benign]. Clinvar id is 771937.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-0.005 with no splicing effect.
BS2
?
High AC in GnomAd at 697 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CDH4 | NM_001794.5 | c.849C>T | p.Asn283= | synonymous_variant | 6/16 | ENST00000614565.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CDH4 | ENST00000614565.5 | c.849C>T | p.Asn283= | synonymous_variant | 6/16 | 1 | NM_001794.5 | P1 | |
CDH4 | ENST00000543233.2 | c.627C>T | p.Asn209= | synonymous_variant | 5/15 | 2 | |||
CDH4 | ENST00000611855.4 | c.567C>T | p.Asn189= | synonymous_variant | 5/15 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00458 AC: 697AN: 152248Hom.: 4 Cov.: 33
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GnomAD3 exomes AF: 0.00416 AC: 1045AN: 251192Hom.: 3 AF XY: 0.00418 AC XY: 567AN XY: 135768
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GnomAD4 exome AF: 0.00552 AC: 8064AN: 1461594Hom.: 29 Cov.: 31 AF XY: 0.00542 AC XY: 3938AN XY: 727100
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GnomAD4 genome ? AF: 0.00457 AC: 697AN: 152364Hom.: 4 Cov.: 33 AF XY: 0.00415 AC XY: 309AN XY: 74520
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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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