rs2446871

Variant names:

• chr8-94152281-C-A
• rs2446871
• NM_004063.4:c.1552-169G>T

Your query was ambiguous. Multiple possible variants found:

• chr8-94152281-C-A
• chr8-94152281-C-G
• chr8-94152281-C-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_004063.4(CDH17):​c.1552-169G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.607 in 152,118 control chromosomes in the GnomAD database, including 29,994 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 0.61 (29994 hom., cov: 33)
• Consequence: CDH17 NM_004063.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.127
• Publications: 2 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=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.84 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.1552-169G>T		intron	N/A	NP_004054.3
	CDH17	NM_001413951.1		c.1609-169G>T		intron	N/A	NP_001400880.1
	CDH17	NM_001144663.2		c.1552-169G>T		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.1552-169G>T		intron	N/A	ENSP00000027335.3	Q12864
	CDH17	ENST00000450165.6	TSL:1	c.1552-169G>T		intron	N/A	ENSP00000401468.2	Q12864
	CDH17	ENST00000877574.1		c.1609-169G>T		intron	N/A	ENSP00000547633.1

Frequencies

GnomAD3 genomes AF: 0.606 AC: 92165 AN: 152000 Hom.: 29941 Cov.: 33

Gnomad AFR AF: 0.847

Gnomad AMI AF: 0.425

Gnomad AMR AF: 0.618

Gnomad ASJ AF: 0.477

Gnomad EAS AF: 0.685

Gnomad SAS AF: 0.604

Gnomad FIN AF: 0.461

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.482

Gnomad OTH AF: 0.630

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

GnomAD4 genome AF: 0.607 AC: 92289 AN: 152118 Hom.: 29994 Cov.: 33 AF XY: 0.609 AC XY: 45268 AN XY: 74354

African (AFR) AF: 0.847 AC: 35171 AN: 41528

American (AMR) AF: 0.619 AC: 9459 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.477 AC: 1652 AN: 3466

East Asian (EAS) AF: 0.685 AC: 3548 AN: 5178

South Asian (SAS) AF: 0.604 AC: 2918 AN: 4830

European-Finnish (FIN) AF: 0.461 AC: 4854 AN: 10534

Middle Eastern (MID) AF: 0.602 AC: 177 AN: 294

European-Non Finnish (NFE) AF: 0.482 AC: 32795 AN: 67976

Other (OTH) AF: 0.630 AC: 1327 AN: 2108

Alfa AF: 0.488 Hom.: 7518

Bravo AF: 0.631

Asia WGS AF: 0.640 AC: 2226 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	3.9
DANN	Benign	0.73
PhyloP100		0.13
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: rs2446871; hg19: chr8-95164509;