chr8-94128296-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_004063.4(CDH17):c.2443G>A(p.Gly815Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000479 in 1,461,172 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_004063.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CDH17 | NM_004063.4 | c.2443G>A | p.Gly815Ser | missense_variant | 18/18 | ENST00000027335.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CDH17 | ENST00000027335.8 | c.2443G>A | p.Gly815Ser | missense_variant | 18/18 | 1 | NM_004063.4 | P1 | |
CDH17 | ENST00000450165.6 | c.2443G>A | p.Gly815Ser | missense_variant | 18/18 | 1 | P1 | ||
CDH17 | ENST00000441892.6 | c.1687G>A | p.Gly563Ser | missense_variant | 13/13 | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.00000399 AC: 1AN: 250912Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135642
GnomAD4 exome AF: 0.00000479 AC: 7AN: 1461172Hom.: 0 Cov.: 29 AF XY: 0.00000688 AC XY: 5AN XY: 726956
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 12, 2023 | The c.2443G>A (p.G815S) alteration is located in exon 18 (coding exon 17) of the CDH17 gene. This alteration results from a G to A substitution at nucleotide position 2443, causing the glycine (G) at amino acid position 815 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at