chr8-94130944-T-G
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_004063.4(CDH17):c.2216A>C(p.Glu739Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.538 in 1,604,310 control chromosomes in the GnomAD database, including 237,689 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_004063.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CDH17 | NM_004063.4 | c.2216A>C | p.Glu739Ala | missense_variant | 16/18 | ENST00000027335.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CDH17 | ENST00000027335.8 | c.2216A>C | p.Glu739Ala | missense_variant | 16/18 | 1 | NM_004063.4 | P1 | |
CDH17 | ENST00000450165.6 | c.2216A>C | p.Glu739Ala | missense_variant | 16/18 | 1 | P1 | ||
CDH17 | ENST00000441892.6 | c.1574A>C | p.Glu525Ala | missense_variant | 12/13 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.479 AC: 72572AN: 151626Hom.: 18594 Cov.: 31
GnomAD3 exomes AF: 0.512 AC: 128225AN: 250280Hom.: 34014 AF XY: 0.518 AC XY: 70047AN XY: 135206
GnomAD4 exome AF: 0.544 AC: 790675AN: 1452568Hom.: 219104 Cov.: 33 AF XY: 0.543 AC XY: 392771AN XY: 723090
GnomAD4 genome ? AF: 0.478 AC: 72582AN: 151742Hom.: 18585 Cov.: 31 AF XY: 0.477 AC XY: 35318AN XY: 74092
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 15, 2020 | This variant is associated with the following publications: (PMID: 23326130) - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at