Variant 18-65822142-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BA1

The NM_004361.5(CDH7):c.687C>T(p.Val229=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.944 in 1,612,670 control chromosomes in the GnomAD database, including 722,369 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.88 ( 59518 hom., cov: 30)

Exomes 𝑓: 0.95 ( 662851 hom. )

Consequence

CDH7
NM_004361.5 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.118

Variant links:

Genes affected

CDH7 (HGNC:1766): (cadherin 7) This gene encodes a type II classical cadherin of the cadherin superfamily. Alternative splicing results in multiple transcript variants, at least one of which encodes a preproprotein that is proteolytically processed to generate the mature glycoprotein. This calcium dependent cell-cell adhesion molecule is 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 histidine-alanine-valine (HAV) cell adhesion recognition sequence specific to type I cadherins. Cadherins mediate cell-cell binding in a homophilic manner, contributing to the sorting of heterogeneous cell types. Mutations in this gene may be associated with bipolar disease in human patients. This gene is present in a gene cluster on chromosome 18. [provided by RefSeq, May 2016]

CDH7 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -19 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.39).

BP6

Variant 18-65822142-C-T is Benign according to our data. Variant chr18-65822142-C-T is described in ClinVar as [Benign]. Clinvar id is 1261986.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-0.118 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.966 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
CDH7	NM_004361.5 linkuse as main transcript	c.687C>T	p.Val229=	synonymous_variant	5/12	ENST00000397968.4
CDH7	NM_001362438.2 linkuse as main transcript	c.687C>T	p.Val229=	synonymous_variant	5/12
CDH7	NM_033646.4 linkuse as main transcript	c.687C>T	p.Val229=	synonymous_variant	5/12
CDH7	NM_001317214.3 linkuse as main transcript	c.687C>T	p.Val229=	synonymous_variant	5/11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris
CDH7	ENST00000397968.4 linkuse as main transcript	c.687C>T	p.Val229=	synonymous_variant	5/12	1	NM_004361.5	P1
CDH7	ENST00000323011.7 linkuse as main transcript	c.687C>T	p.Val229=	synonymous_variant	5/12	1		P1
CDH7	ENST00000536984.6 linkuse as main transcript	c.687C>T	p.Val229=	synonymous_variant	5/11	1

Frequencies

GnomAD3 genomes

AF:

0.876

AC:

132992

AN:

151874

Hom.:

59483

Cov.:

show subpopulations

Gnomad AFR

AF:

0.673

Gnomad AMI

AF:

0.878

Gnomad AMR

AF:

0.925

Gnomad ASJ

AF:

0.905

Gnomad EAS

AF:

0.989

Gnomad SAS

AF:

0.875

Gnomad FIN

AF:

0.968

Gnomad MID

AF:

0.899

Gnomad NFE

AF:

0.962

Gnomad OTH

AF:

0.895

GnomAD3 exomes

AF:

0.930

AC:

233665

AN:

251304

Hom.:

109436

AF XY:

0.932

AC XY:

126615

AN XY:

135844

show subpopulations

Gnomad AFR exome

AF:

0.670

Gnomad AMR exome

AF:

0.936

Gnomad ASJ exome

AF:

0.906

Gnomad EAS exome

AF:

0.990

Gnomad SAS exome

AF:

0.879

Gnomad FIN exome

AF:

0.970

Gnomad NFE exome

AF:

0.963

Gnomad OTH exome

AF:

0.945

GnomAD4 exome

AF:

0.951

AC:

1389268

AN:

1460678

Hom.:

662851

Cov.:

AF XY:

0.950

AC XY:

690316

AN XY:

726734

show subpopulations

Gnomad4 AFR exome

AF:

0.653

Gnomad4 AMR exome

AF:

0.932

Gnomad4 ASJ exome

AF:

0.905

Gnomad4 EAS exome

AF:

0.990

Gnomad4 SAS exome

AF:

0.884

Gnomad4 FIN exome

AF:

0.971

Gnomad4 NFE exome

AF:

0.966

Gnomad4 OTH exome

AF:

0.933

GnomAD4 genome

AF:

0.876

AC:

133076

AN:

151992

Hom.:

59518

Cov.:

AF XY:

0.878

AC XY:

65203

AN XY:

74300

show subpopulations

Gnomad4 AFR

AF:

0.673

Gnomad4 AMR

AF:

0.926

Gnomad4 ASJ

AF:

0.905

Gnomad4 EAS

AF:

0.989

Gnomad4 SAS

AF:

0.875

Gnomad4 FIN

AF:

0.968

Gnomad4 NFE

AF:

0.962

Gnomad4 OTH

AF:

0.895

Alfa

AF:

0.945

Hom.:

152511

Bravo

AF:

0.863

Asia WGS

AF:

0.883

AC:

3071

AN:

3478

EpiCase

AF:

0.959

EpiControl

AF:

0.956

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Nov 10, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.39

CADD

Benign

DANN

Benign

0.74

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

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