Variant 18-61507422-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2

The NM_031891.4(CDH20):c.879C>T(p.Val293Val) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00403 in 1,614,020 control chromosomes in the GnomAD database, including 19 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0027 ( 1 hom., cov: 32)

Exomes 𝑓: 0.0042 ( 18 hom. )

Consequence

CDH20
NM_031891.4 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 3.33

Variant links:

Genes affected

CDH20 (HGNC:1760): (cadherin 20) This gene is a type II classical cadherin from the cadherin superfamily and one of three cadherin 7-like genes located in a cluster on chromosome 18. The encoded membrane protein is a calcium dependent cell-cell adhesion glycoprotein comprised of five extracellular cadherin repeats, a transmembrane region and a highly conserved cytoplasmic tail. Type II (atypical) cadherins are defined based on their lack of a HAV cell adhesion recognition sequence specific to type I cadherins. Since disturbance of intracellular adhesion is a prerequisite for invasion and metastasis of tumor cells, cadherins are considered prime candidates for tumor suppressor genes. [provided by RefSeq, Jul 2008]

CDH20 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -9 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.2).

BP6

Variant 18-61507422-C-T is Benign according to our data. Variant chr18-61507422-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2648772.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=3.33 with no splicing effect.

BS2

High Homozygotes in GnomAdExome4 at 18 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CDH20	NM_031891.4 link	c.879C>T	p.Val293Val	synonymous_variant	6/12	ENST00000262717.9	NP_114097.2	Q9HBT6A8K2C5Q8N9J3
CDH20	XM_024451165.2 link	c.879C>T	p.Val293Val	synonymous_variant	6/12		XP_024306933.1
CDH20	XR_001753186.2 link	n.1429C>T		non_coding_transcript_exon_variant	6/11
CDH20	XR_001753187.2 link	n.1429C>T		non_coding_transcript_exon_variant	6/12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
CDH20	ENST00000262717.9 link	c.879C>T	p.Val293Val	synonymous_variant	6/12	2	NM_031891.4	ENSP00000262717.3	Q9HBT6
CDH20	ENST00000536675.2 link	c.879C>T	p.Val293Val	synonymous_variant	5/11	1		ENSP00000444767.1	Q9HBT6
CDH20	ENST00000538374.5 link	c.879C>T	p.Val293Val	synonymous_variant	6/12	1		ENSP00000442226.1	Q9HBT6

Frequencies

GnomAD3 genomes

AF:

0.00273

AC:

416

AN:

152122

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000917

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00190

Gnomad ASJ

AF:

0.00980

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00166

Gnomad FIN

AF:

0.000755

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.00434

Gnomad OTH

AF:

0.00143

GnomAD3 exomes

AF:

0.00282

AC:

710

AN:

251330

Hom.:

AF XY:

0.00300

AC XY:

407

AN XY:

135828

show subpopulations

Gnomad AFR exome

AF:

0.000554

Gnomad AMR exome

AF:

0.00130

Gnomad ASJ exome

AF:

0.00665

Gnomad EAS exome

AF:

0.0000544

Gnomad SAS exome

AF:

0.00209

Gnomad FIN exome

AF:

0.00111

Gnomad NFE exome

AF:

0.00424

Gnomad OTH exome

AF:

0.00293

GnomAD4 exome

AF:

0.00416

AC:

6083

AN:

1461780

Hom.:

Cov.:

AF XY:

0.00415

AC XY:

3018

AN XY:

727186

show subpopulations

Gnomad4 AFR exome

AF:

0.000627

Gnomad4 AMR exome

AF:

0.00139

Gnomad4 ASJ exome

AF:

0.00708

Gnomad4 EAS exome

AF:

0.0000504

Gnomad4 SAS exome

AF:

0.00165

Gnomad4 FIN exome

AF:

0.000973

Gnomad4 NFE exome

AF:

0.00485

Gnomad4 OTH exome

AF:

0.00356

GnomAD4 genome

AF:

0.00273

AC:

416

AN:

152240

Hom.:

Cov.:

AF XY:

0.00269

AC XY:

200

AN XY:

74428

show subpopulations

Gnomad4 AFR

AF:

0.000914

Gnomad4 AMR

AF:

0.00190

Gnomad4 ASJ

AF:

0.00980

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00166

Gnomad4 FIN

AF:

0.000755

Gnomad4 NFE

AF:

0.00434

Gnomad4 OTH

AF:

0.00142

Alfa

AF:

0.00428

Hom.:

Bravo

AF:

0.00301

Asia WGS

AF:

0.000866

AC:

AN:

3478

EpiCase

AF:

0.00404

EpiControl

AF:

0.00468

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Jan 01, 2023

CDH20: BP4, BP7, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.20

CADD

Benign

9.7

DANN

Benign

0.73

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over