rs1126933
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP7
The NM_001793.6(CDH3):c.1689G>A(p.Gln563=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000186 in 1,613,770 control chromosomes in the GnomAD database, with no homozygous occurrence. 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
Consequence
NM_001793.6 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CDH3 | NM_001793.6 | c.1689G>A | p.Gln563= | synonymous_variant | 12/16 | ENST00000264012.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CDH3 | ENST00000264012.9 | c.1689G>A | p.Gln563= | synonymous_variant | 12/16 | 1 | NM_001793.6 | P1 | |
CDH3 | ENST00000429102.6 | c.1689G>A | p.Gln563= | synonymous_variant | 12/16 | 1 | |||
CDH3 | ENST00000567674.1 | c.12G>A | p.Gln4= | synonymous_variant, NMD_transcript_variant | 1/5 | 3 | |||
CDH3 | ENST00000542274.5 | c.*1427G>A | 3_prime_UTR_variant, NMD_transcript_variant | 11/15 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000132 AC: 2AN: 151934Hom.: 0 Cov.: 30
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461836Hom.: 0 Cov.: 43 AF XY: 0.00 AC XY: 0AN XY: 727224
GnomAD4 genome ? AF: 0.0000132 AC: 2AN: 151934Hom.: 0 Cov.: 30 AF XY: 0.0000270 AC XY: 2AN XY: 74164
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at