rs2298574
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001792.5(CDH2):c.1599-428T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0691 in 152,266 control chromosomes in the GnomAD database, including 400 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 0.069 ( 400 hom., cov: 32)
Consequence
CDH2
NM_001792.5 intron
NM_001792.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.0820
Genes affected
CDH2 (HGNC:1759): (cadherin 2) This gene encodes a classical cadherin and member of the cadherin superfamily. Alternative splicing results in multiple transcript variants, at least one of which encodes a preproprotein is proteolytically processed to generate a calcium-dependent cell adhesion molecule and glycoprotein. This protein plays a role in the establishment of left-right asymmetry, development of the nervous system and the formation of cartilage and bone. [provided by RefSeq, Nov 2015]
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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=-0.83).
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0837 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CDH2 | NM_001792.5 | c.1599-428T>C | intron_variant | ENST00000269141.8 | |||
CDH2 | NM_001308176.2 | c.1506-428T>C | intron_variant | ||||
CDH2 | XM_011525788.1 | c.1344-428T>C | intron_variant | ||||
CDH2 | XM_017025514.3 | c.1599-428T>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CDH2 | ENST00000269141.8 | c.1599-428T>C | intron_variant | 1 | NM_001792.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0692 AC: 10532AN: 152146Hom.: 400 Cov.: 32
GnomAD3 genomes
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152146
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32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.0691 AC: 10523AN: 152266Hom.: 400 Cov.: 32 AF XY: 0.0694 AC XY: 5169AN XY: 74452
GnomAD4 genome
?
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10523
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32
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5169
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74452
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173
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3476
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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