rs863224397
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP7
The NM_004360.5(CDH1):c.690C>A(p.Leu230=) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 1/1 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. L230L) has been classified as Likely benign.
Frequency
Consequence
NM_004360.5 splice_region, synonymous
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CDH1 | NM_004360.5 | c.690C>A | p.Leu230= | splice_region_variant, synonymous_variant | 6/16 | ENST00000261769.10 | |
CDH1 | NM_001317184.2 | c.690C>A | p.Leu230= | splice_region_variant, synonymous_variant | 6/15 | ||
CDH1 | NM_001317185.2 | c.-926C>A | splice_region_variant, 5_prime_UTR_variant | 6/16 | |||
CDH1 | NM_001317186.2 | c.-1130C>A | splice_region_variant, 5_prime_UTR_variant | 6/15 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CDH1 | ENST00000261769.10 | c.690C>A | p.Leu230= | splice_region_variant, synonymous_variant | 6/16 | 1 | NM_004360.5 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome Cov.: 32
GnomAD4 genome ? Cov.: 32
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.