rs10485464

Variant names:

• chr20-60002616-A-C
• rs10485464
• NM_177980.4:c.2167-197A>C

Your query was ambiguous. Multiple possible variants found:

• chr20-60002616-A-C
• chr20-60002616-A-G

Variant summary

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

The NM_177980.4(CDH26):​c.2167-197A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0597 in 152,076 control chromosomes in the GnomAD database, including 628 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 0.060 (628 hom., cov: 32)
• Consequence: CDH26 NM_177980.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.428
• Publications: 2 publications found

Genes affected

CDH26 (HGNC:15902): (cadherin 26) This gene encodes a member of the cadherin protein family. Cadherins are a family of calcium-dependent adhesion molecules that mediate cell-cell adhesion in all solid tissues and modulate a wide variety of processes, including cell polarization, migration and differentiation. Cadherin domains occur as repeats in the extracellular region and are thought to contribute to the sorting of heterogeneous cell types and the maintenance of orderly structures such as epithelium. This protein is expressed in gastrointestinal epithelial cells and may be upregulated during allergic inflammation. This protein interacts with alpha integrins and may also be involved in leukocyte migration and adhesion. [provided by RefSeq, Jan 2017]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.165 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CDH26	NM_177980.4	c.2167-197A>C		intron_variant	Intron 15 of 17	ENST00000348616.9	NP_817089.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CDH26	ENST00000348616.9	c.2167-197A>C		intron_variant	Intron 15 of 17	2	NM_177980.4	ENSP00000339390.4

Frequencies

GnomAD3 genomes AF: 0.0594 AC: 9030 AN: 151958 Hom.: 622 Cov.: 32

Gnomad AFR AF: 0.168

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0247

Gnomad ASJ AF: 0.0276

Gnomad EAS AF: 0.0509

Gnomad SAS AF: 0.0579

Gnomad FIN AF: 0.0194

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0109

Gnomad OTH AF: 0.0533

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

GnomAD4 genome AF: 0.0597 AC: 9080 AN: 152076 Hom.: 628 Cov.: 32 AF XY: 0.0596 AC XY: 4434 AN XY: 74334

African (AFR) AF: 0.169 AC: 6994 AN: 41468

American (AMR) AF: 0.0245 AC: 375 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0276 AC: 96 AN: 3472

East Asian (EAS) AF: 0.0510 AC: 261 AN: 5114

South Asian (SAS) AF: 0.0582 AC: 280 AN: 4814

European-Finnish (FIN) AF: 0.0194 AC: 206 AN: 10598

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.0109 AC: 744 AN: 68018

Other (OTH) AF: 0.0547 AC: 115 AN: 2104

Alfa AF: 0.0246 Hom.: 107

Bravo AF: 0.0635

Asia WGS AF: 0.0750 AC: 261 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.56
DANN	Benign	0.46
PhyloP100		-0.43
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: rs10485464; hg19: chr20-58577671;