chr8-94148752-G-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_004063.4(CDH17):c.1919C>G(p.Thr640Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000256 in 992,202 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 Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CDH17 | NM_004063.4 | c.1919C>G | p.Thr640Arg | missense_variant | 14/18 | ENST00000027335.8 | |
LOC105375647 | XR_007061012.1 | n.518+4479G>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CDH17 | ENST00000027335.8 | c.1919C>G | p.Thr640Arg | missense_variant | 14/18 | 1 | NM_004063.4 | P1 | |
CDH17 | ENST00000450165.6 | c.1919C>G | p.Thr640Arg | missense_variant | 14/18 | 1 | P1 | ||
CDH17 | ENST00000441892.6 | c.1277C>G | p.Thr426Arg | missense_variant | 10/13 | 2 | |||
CDH17 | ENST00000520952.1 | c.*87C>G | 3_prime_UTR_variant, NMD_transcript_variant | 3/4 | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.000113 AC: 11AN: 97022Hom.: 0 Cov.: 23
GnomAD3 exomes AF: 0.0000441 AC: 7AN: 158580Hom.: 0 AF XY: 0.0000458 AC XY: 4AN XY: 87368
GnomAD4 exome AF: 0.000271 AC: 243AN: 895180Hom.: 0 Cov.: 30 AF XY: 0.000267 AC XY: 119AN XY: 445744
GnomAD4 genome ? AF: 0.000113 AC: 11AN: 97022Hom.: 0 Cov.: 23 AF XY: 0.0000895 AC XY: 4AN XY: 44672
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 26, 2023 | The c.1919C>G (p.T640R) alteration is located in exon 14 (coding exon 13) of the CDH17 gene. This alteration results from a C to G substitution at nucleotide position 1919, causing the threonine (T) at amino acid position 640 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