rs58548890
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_004360.5(CDH1):c.163+19370_163+19381del variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.00019 ( 1 hom., cov: 0)
Consequence
CDH1
NM_004360.5 intron
NM_004360.5 intron
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.460
Genes affected
CDH1 (HGNC:1748): (cadherin 1) This gene encodes a classical cadherin of the cadherin superfamily. Alternative splicing results in multiple transcript variants, at least one of which encodes a preproprotein that is proteolytically processed to generate the mature glycoprotein. This calcium-dependent cell-cell adhesion protein is comprised of five extracellular cadherin repeats, a transmembrane region and a highly conserved cytoplasmic tail. Mutations in this gene are correlated with gastric, breast, colorectal, thyroid and ovarian cancer. Loss of function of this gene is thought to contribute to cancer progression by increasing proliferation, invasion, and/or metastasis. The ectodomain of this protein mediates bacterial adhesion to mammalian cells and the cytoplasmic domain is required for internalization. This gene is present in a gene cluster with other members of the cadherin family on chromosome 16. [provided by RefSeq, Nov 2015]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
BS2
?
High AC in GnomAd4 at 28 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CDH1 | NM_004360.5 | c.163+19370_163+19381del | intron_variant | ENST00000261769.10 | |||
CDH1 | NM_001317184.2 | c.163+19370_163+19381del | intron_variant | ||||
CDH1 | NM_001317185.2 | c.-1453+19370_-1453+19381del | intron_variant | ||||
CDH1 | NM_001317186.2 | c.-1657+19370_-1657+19381del | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CDH1 | ENST00000261769.10 | c.163+19370_163+19381del | intron_variant | 1 | NM_004360.5 | P1 | |||
CDH1 | ENST00000422392.6 | c.163+19370_163+19381del | intron_variant | 1 | |||||
CDH1 | ENST00000566612.5 | c.163+19370_163+19381del | intron_variant, NMD_transcript_variant | 1 | |||||
CDH1 | ENST00000566510.5 | c.163+19370_163+19381del | intron_variant, NMD_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.000169 AC: 25AN: 147916Hom.: 0 Cov.: 0
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GnomAD4 genome ? AF: 0.000189 AC: 28AN: 148034Hom.: 1 Cov.: 0 AF XY: 0.000223 AC XY: 16AN XY: 71888
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ClinVar
Not reported inComputational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at