chr8-94151866-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_004063.4(CDH17):c.1796+2T>C variant causes a splice donor change. The variant allele was found at a frequency of 0.0000756 in 1,613,842 control chromosomes in the GnomAD database, including 1 homozygotes. 2/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.000020 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000081 ( 1 hom. )
Consequence
CDH17
NM_004063.4 splice_donor
NM_004063.4 splice_donor
Scores
4
2
1
Splicing: ADA: 0.9923
1
1
Clinical Significance
Conservation
PhyloP100: 6.73
Genes affected
CDH17 (HGNC:1756): (cadherin 17) This gene is a member of the cadherin superfamily, genes encoding calcium-dependent, membrane-associated glycoproteins. The encoded protein is cadherin-like, consisting of an extracellular region, containing 7 cadherin domains, and a transmembrane region but lacking the conserved cytoplasmic domain. The protein is a component of the gastrointestinal tract and pancreatic ducts, acting as an intestinal proton-dependent peptide transporter in the first step in oral absorption of many medically important peptide-based drugs. The protein may also play a role in the morphological organization of liver and intestine. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2009]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CDH17 | NM_004063.4 | c.1796+2T>C | splice_donor_variant | ENST00000027335.8 | |||
LOC105375647 | XR_007061012.1 | n.518+7593A>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CDH17 | ENST00000027335.8 | c.1796+2T>C | splice_donor_variant | 1 | NM_004063.4 | P1 | |||
CDH17 | ENST00000450165.6 | c.1796+2T>C | splice_donor_variant | 1 | P1 | ||||
CDH17 | ENST00000441892.6 | c.1154+2T>C | splice_donor_variant | 2 | |||||
CDH17 | ENST00000520952.1 | c.236-2992T>C | intron_variant, NMD_transcript_variant | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152024Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000996 AC: 25AN: 251062Hom.: 0 AF XY: 0.000133 AC XY: 18AN XY: 135712
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GnomAD4 exome AF: 0.0000814 AC: 119AN: 1461818Hom.: 1 Cov.: 32 AF XY: 0.0000990 AC XY: 72AN XY: 727214
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GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152024Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74270
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Oct 01, 2018 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Uncertain
D
BayesDel_noAF
Pathogenic
Cadd
Pathogenic
Dann
Uncertain
Eigen
Pathogenic
Eigen_PC
Pathogenic
FATHMM_MKL
Pathogenic
D
MutationTaster
Benign
D;D;D
GERP RS
Splicing
Name
Calibrated prediction
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dbscSNV1_ADA
Pathogenic
dbscSNV1_RF
Benign
SpliceAI score (max)
Details are displayed if max score is > 0.2
DS_DL_spliceai
Position offset: 2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at