rs16985493
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001794.5(CDH4):c.170-25056G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0455 in 317,434 control chromosomes in the GnomAD database, including 442 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.053 ( 256 hom., cov: 34)
Exomes 𝑓: 0.039 ( 186 hom. )
Consequence
CDH4
NM_001794.5 intron
NM_001794.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.348
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 -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-1.03).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.073 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CDH4 | NM_001794.5 | c.170-25056G>A | intron_variant | ENST00000614565.5 | |||
LOC100128310 | NR_147702.1 | n.999C>T | non_coding_transcript_exon_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CDH4 | ENST00000614565.5 | c.170-25056G>A | intron_variant | 1 | NM_001794.5 | P1 | |||
ENST00000317652.1 | n.999C>T | non_coding_transcript_exon_variant | 2/2 | 2 | |||||
CDH4 | ENST00000543233.2 | c.-53-25056G>A | intron_variant | 2 | |||||
CDH4 | ENST00000611855.4 | c.50-25056G>A | intron_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0530 AC: 8069AN: 152184Hom.: 254 Cov.: 34
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GnomAD4 exome AF: 0.0387 AC: 6386AN: 165132Hom.: 186 Cov.: 0 AF XY: 0.0352 AC XY: 3112AN XY: 88408
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GnomAD4 genome ? AF: 0.0530 AC: 8068AN: 152302Hom.: 256 Cov.: 34 AF XY: 0.0496 AC XY: 3692AN XY: 74478
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ClinVar
Not reported inComputational 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