rs11776675

Variant names:

• chr8-94163787-T-C
• rs11776675
• NM_004063.4:c.1283-1625A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

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]

ENSG00000304524 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_004063.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CDH17	NM_004063.4	MANE Select	c.1283-1625A>G		intron	N/A	NP_004054.3
	CDH17	NM_001413951.1		c.1340-1625A>G		intron	N/A	NP_001400880.1
	CDH17	NM_001144663.2		c.1283-1625A>G		intron	N/A	NP_001138135.1	Q12864

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CDH17	ENST00000027335.8	TSL:1 MANE Select	c.1283-1625A>G		intron	N/A	ENSP00000027335.3	Q12864
	CDH17	ENST00000450165.6	TSL:1	c.1283-1625A>G		intron	N/A	ENSP00000401468.2	Q12864
	CDH17	ENST00000877574.1		c.1340-1625A>G		intron	N/A	ENSP00000547633.1

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

African (AFR) AF: 0.0725 AC: 3011 AN: 41548

American (AMR) AF: 0.203 AC: 3097 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.353 AC: 1224 AN: 3470

East Asian (EAS) AF: 0.118 AC: 609 AN: 5166

South Asian (SAS) AF: 0.367 AC: 1764 AN: 4810

European-Finnish (FIN) AF: 0.282 AC: 2979 AN: 10574

Middle Eastern (MID) AF: 0.306 AC: 90 AN: 294

European-Non Finnish (NFE) AF: 0.326 AC: 22153 AN: 67956

Other (OTH) AF: 0.259 AC: 546 AN: 2110

Alfa AF: 0.296 Hom.: 9027

Bravo AF: 0.221

Asia WGS AF: 0.231 AC: 803 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.3
DANN	Benign	0.47
PhyloP100		-0.066
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs11776675; hg19: chr8-95176015;