rs1555515331
Variant summary
Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PVS1PM2PP5
The NM_001797.4(CDH11):c.999+1G>T variant causes a splice donor, intron change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000000688 in 1,453,076 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 3/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Pathogenic (no stars).
Frequency
Consequence
NM_001797.4 splice_donor, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CDH11 | NM_001797.4 | c.999+1G>T | splice_donor_variant, intron_variant | Intron 7 of 12 | ENST00000268603.9 | NP_001788.2 | ||
CDH11 | NM_001308392.2 | c.999+1G>T | splice_donor_variant, intron_variant | Intron 7 of 13 | NP_001295321.1 | |||
CDH11 | NM_001330576.2 | c.621+1G>T | splice_donor_variant, intron_variant | Intron 6 of 11 | NP_001317505.1 | |||
CDH11 | XM_047433486.1 | c.621+1G>T | splice_donor_variant, intron_variant | Intron 6 of 11 | XP_047289442.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CDH11 | ENST00000268603.9 | c.999+1G>T | splice_donor_variant, intron_variant | Intron 7 of 12 | 1 | NM_001797.4 | ENSP00000268603.4 | |||
CDH11 | ENST00000394156.7 | c.999+1G>T | splice_donor_variant, intron_variant | Intron 7 of 13 | 1 | ENSP00000377711.3 | ||||
CDH11 | ENST00000619158.1 | c.178G>T | p.Val60Leu | missense_variant | Exon 1 of 1 | 6 | ENSP00000484650.1 | |||
CDH11 | ENST00000566827.5 | c.621+1G>T | splice_donor_variant, intron_variant | Intron 6 of 11 | 2 | ENSP00000457812.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 6.88e-7 AC: 1AN: 1453076Hom.: 0 Cov.: 29 AF XY: 0.00 AC XY: 0AN XY: 722444
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Elsahy-Waters syndrome Pathogenic:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at