chr8-94148783-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.1888G>A(p.Gly630Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000583 in 1,594,018 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 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.1888G>A | p.Gly630Arg | missense_variant | 14/18 | ENST00000027335.8 | |
LOC105375647 | XR_007061012.1 | n.518+4510C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CDH17 | ENST00000027335.8 | c.1888G>A | p.Gly630Arg | missense_variant | 14/18 | 1 | NM_004063.4 | P1 | |
CDH17 | ENST00000450165.6 | c.1888G>A | p.Gly630Arg | missense_variant | 14/18 | 1 | P1 | ||
CDH17 | ENST00000441892.6 | c.1246G>A | p.Gly416Arg | missense_variant | 10/13 | 2 | |||
CDH17 | ENST00000520952.1 | c.*56G>A | 3_prime_UTR_variant, NMD_transcript_variant | 3/4 | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000610 AC: 9AN: 147482Hom.: 0 Cov.: 29
GnomAD3 exomes AF: 0.000129 AC: 31AN: 240344Hom.: 0 AF XY: 0.000138 AC XY: 18AN XY: 130082
GnomAD4 exome AF: 0.0000581 AC: 84AN: 1446438Hom.: 0 Cov.: 33 AF XY: 0.0000667 AC XY: 48AN XY: 719414
GnomAD4 genome ? AF: 0.0000610 AC: 9AN: 147580Hom.: 0 Cov.: 29 AF XY: 0.0000699 AC XY: 5AN XY: 71542
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 30, 2023 | The c.1888G>A (p.G630R) alteration is located in exon 14 (coding exon 13) of the CDH17 gene. This alteration results from a G to A substitution at nucleotide position 1888, causing the glycine (G) at amino acid position 630 to be replaced by an arginine (R). 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