rs2514805

Positions:

• chr8-94155019-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_004063.4(CDH17):​c.1552-2907T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0975 in 152,098 control chromosomes in the GnomAD database, including 811 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.098 (811 hom., cov: 31)
• Consequence: CDH17 NM_004063.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.298

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]

CDH17 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.114 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CDH17	NM_004063.4	c.1552-2907T>C		intron_variant		ENST00000027335.8	NP_004054.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CDH17	ENST00000027335.8	c.1552-2907T>C		intron_variant		1	NM_004063.4	ENSP00000027335.3
CDH17	ENST00000450165.6	c.1552-2907T>C		intron_variant		1		ENSP00000401468.2
CDH17	ENST00000441892.6	c.910-2907T>C		intron_variant		2		ENSP00000392811.2
CDH17	ENST00000520952.1	n.234+4952T>C		intron_variant		4		ENSP00000429730.1

Frequencies

GnomAD3 genomes AF: 0.0974 AC: 14804 AN: 151980 Hom.: 804 Cov.: 31

Gnomad AFR AF: 0.0724

Gnomad AMI AF: 0.115

Gnomad AMR AF: 0.0920

Gnomad ASJ AF: 0.143

Gnomad EAS AF: 0.000775

Gnomad SAS AF: 0.0616

Gnomad FIN AF: 0.125

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.116

Gnomad OTH AF: 0.119

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0975 AC: 14833 AN: 152098 Hom.: 811 Cov.: 31 AF XY: 0.0972 AC XY: 7229 AN XY: 74344

Gnomad4 AFR AF: 0.0729

Gnomad4 AMR AF: 0.0917

Gnomad4 ASJ AF: 0.143

Gnomad4 EAS AF: 0.000777

Gnomad4 SAS AF: 0.0623

Gnomad4 FIN AF: 0.125

Gnomad4 NFE AF: 0.116

Gnomad4 OTH AF: 0.117

Alfa AF: 0.108 Hom.: 393

Bravo AF: 0.0946

Asia WGS AF: 0.0370 AC: 129 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.0
DANN	Benign	0.35

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs2514805; hg19: chr8-95167247;