chr8-94130660-T-C
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 2P and 13B. PM2BP4_StrongBP6_Very_StrongBP7
The NM_004063.4(CDH17):c.2364A>G(p.Ala788=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000477 in 1,613,702 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.0026 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00026 ( 1 hom. )
Consequence
CDH17
NM_004063.4 synonymous
NM_004063.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.206
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 Benign. Variant got -11 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.58).
BP6
?
Variant 8-94130660-T-C is Benign according to our data. Variant chr8-94130660-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 720737.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
?
Synonymous conserved (PhyloP=-0.206 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CDH17 | NM_004063.4 | c.2364A>G | p.Ala788= | synonymous_variant | 17/18 | ENST00000027335.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CDH17 | ENST00000027335.8 | c.2364A>G | p.Ala788= | synonymous_variant | 17/18 | 1 | NM_004063.4 | P1 | |
CDH17 | ENST00000450165.6 | c.2364A>G | p.Ala788= | synonymous_variant | 17/18 | 1 | P1 | ||
CDH17 | ENST00000441892.6 | c.1642+216A>G | intron_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00258 AC: 393AN: 152190Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000666 AC: 167AN: 250836Hom.: 1 AF XY: 0.000465 AC XY: 63AN XY: 135530
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GnomAD4 exome AF: 0.000259 AC: 378AN: 1461394Hom.: 1 Cov.: 30 AF XY: 0.000235 AC XY: 171AN XY: 726960
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GnomAD4 genome ? AF: 0.00257 AC: 392AN: 152308Hom.: 0 Cov.: 32 AF XY: 0.00250 AC XY: 186AN XY: 74478
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Apr 01, 2022 | CDH17: BP4, BP7 - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at