rs11776675

chr8-94163787-T-C

Variant summary

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

The NM_004063.4(CDH17):c.1283-1625A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.235 in 152,130 control chromosomes in the GnomAD database, including 5,217 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 0.23 (5217 hom., cov: 33)
• Consequence: CDH17 NM_004063.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0660

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]

LOC105375647 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.352 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CDH17	NM_004063.4	c.1283-1625A>G		intron_variant		ENST00000027335.8
LOC105375647	XR_007061012.1	n.519-2432T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CDH17	ENST00000027335.8	c.1283-1625A>G		intron_variant		1	NM_004063.4	P1
CDH17	ENST00000450165.6	c.1283-1625A>G		intron_variant		1		P1
CDH17	ENST00000441892.6	c.641-1625A>G		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.235 AC: 35716 AN: 152012 Hom.: 5214 Cov.: 33

Gnomad AFR AF: 0.0726

Gnomad AMI AF: 0.270

Gnomad AMR AF: 0.203

Gnomad ASJ AF: 0.353

Gnomad EAS AF: 0.118

Gnomad SAS AF: 0.365

Gnomad FIN AF: 0.282

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.326

Gnomad OTH AF: 0.260

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

GnomAD4 genome AF: 0.235 AC: 35719 AN: 152130 Hom.: 5217 Cov.: 33 AF XY: 0.235 AC XY: 17465 AN XY: 74362

Gnomad4 AFR AF: 0.0725

Gnomad4 AMR AF: 0.203

Gnomad4 ASJ AF: 0.353

Gnomad4 EAS AF: 0.118

Gnomad4 SAS AF: 0.367

Gnomad4 FIN AF: 0.282

Gnomad4 NFE AF: 0.326

Gnomad4 OTH AF: 0.259

Alfa AF: 0.306 Hom.: 7271

Bravo AF: 0.221

Asia WGS AF: 0.231 AC: 803 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	3.3
Dann	Benign	0.47

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: rs11776675; hg19: chr8-95176015;