chr8-94145974-G-A
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_StrongBP6_ModerateBP7
The NM_004063.4(CDH17):c.2121C>T(p.Leu707=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000636 in 1,613,576 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0017 ( 1 hom., cov: 32)
Exomes 𝑓: 0.00053 ( 1 hom. )
Consequence
CDH17
NM_004063.4 synonymous
NM_004063.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.08
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 -7 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.75).
BP6
?
Variant 8-94145974-G-A is Benign according to our data. Variant chr8-94145974-G-A is described in ClinVar as [Benign]. Clinvar id is 730578.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-1.08 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CDH17 | NM_004063.4 | c.2121C>T | p.Leu707= | synonymous_variant | 15/18 | ENST00000027335.8 | |
LOC105375647 | XR_007061012.1 | n.518+1701G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CDH17 | ENST00000027335.8 | c.2121C>T | p.Leu707= | synonymous_variant | 15/18 | 1 | NM_004063.4 | P1 | |
CDH17 | ENST00000450165.6 | c.2121C>T | p.Leu707= | synonymous_variant | 15/18 | 1 | P1 | ||
CDH17 | ENST00000441892.6 | c.1479C>T | p.Leu493= | synonymous_variant | 11/13 | 2 | |||
CDH17 | ENST00000520952.1 | c.*289C>T | 3_prime_UTR_variant, NMD_transcript_variant | 4/4 | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.00166 AC: 252AN: 152078Hom.: 1 Cov.: 32
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GnomAD3 exomes AF: 0.000662 AC: 166AN: 250574Hom.: 0 AF XY: 0.000569 AC XY: 77AN XY: 135398
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GnomAD4 exome AF: 0.000530 AC: 775AN: 1461380Hom.: 1 Cov.: 32 AF XY: 0.000490 AC XY: 356AN XY: 726978
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | May 31, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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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