Variant chr18-27952116-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -18 ACMG points: 0P and 18B. BP4_ModerateBP6_Very_StrongBA1

The ENST00000269141.8(CDH2):c.*37C>T variant causes a 3 prime UTR change. The variant allele was found at a frequency of 0.0684 in 1,528,194 control chromosomes in the GnomAD database, including 4,058 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.083 ( 644 hom., cov: 32)

Exomes 𝑓: 0.067 ( 3414 hom. )

Consequence

CDH2
ENST00000269141.8 3_prime_UTR

Scores

Clinical Significance

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

Conservation

PhyloP100: 5.91

Variant links:

Genes affected

CDH2 (HGNC:1759): (cadherin 2) This gene encodes a classical cadherin and member of the cadherin superfamily. Alternative splicing results in multiple transcript variants, at least one of which encodes a preproprotein is proteolytically processed to generate a calcium-dependent cell adhesion molecule and glycoprotein. This protein plays a role in the establishment of left-right asymmetry, development of the nervous system and the formation of cartilage and bone. [provided by RefSeq, Nov 2015]

CDH2 links:

(HGNC:):

links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -18 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.19).

BP6

Variant 18-27952116-G-A is Benign according to our data. Variant chr18-27952116-G-A is described in ClinVar as [Benign]. Clinvar id is 1286608.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.138 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons	MANE	Protein
CDH2	NM_001792.5 linkuse as main transcript	c.*37C>T	3_prime_UTR_variant	16/16	ENST00000269141.8	NP_001783.2
CDH2	NM_001308176.2 linkuse as main transcript	c.*37C>T	3_prime_UTR_variant	15/15		NP_001295105.1
CDH2	XM_011525788.1 linkuse as main transcript	c.*37C>T	3_prime_UTR_variant	16/16		XP_011524090.1
CDH2	XM_017025514.3 linkuse as main transcript	c.2514+11241C>T	intron_variant			XP_016881003.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CDH2	ENST00000269141.8 linkuse as main transcript	c.*37C>T		3_prime_UTR_variant	16/16	1	NM_001792.5	ENSP00000269141	P1	P19022-1
	ENST00000423367.2 linkuse as main transcript	n.199-2402G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes

AF:

0.0829

AC:

12604

AN:

152010

Hom.:

640

Cov.:

show subpopulations

Gnomad AFR

AF:

0.141

Gnomad AMI

AF:

0.0888

Gnomad AMR

AF:

0.0501

Gnomad ASJ

AF:

0.0948

Gnomad EAS

AF:

0.0481

Gnomad SAS

AF:

0.0995

Gnomad FIN

AF:

0.0400

Gnomad MID

AF:

0.0759

Gnomad NFE

AF:

0.0630

Gnomad OTH

AF:

0.0722

GnomAD3 exomes

AF:

0.0667

AC:

16713

AN:

250488

Hom.:

722

AF XY:

0.0678

AC XY:

9174

AN XY:

135368

show subpopulations

Gnomad AFR exome

AF:

0.145

Gnomad AMR exome

AF:

0.0320

Gnomad ASJ exome

AF:

0.0938

Gnomad EAS exome

AF:

0.0507

Gnomad SAS exome

AF:

0.0956

Gnomad FIN exome

AF:

0.0402

Gnomad NFE exome

AF:

0.0636

Gnomad OTH exome

AF:

0.0629

GnomAD4 exome

AF:

0.0668

AC:

91855

AN:

1376066

Hom.:

3414

Cov.:

AF XY:

0.0676

AC XY:

46612

AN XY:

689834

show subpopulations

Gnomad4 AFR exome

AF:

0.146

Gnomad4 AMR exome

AF:

0.0343

Gnomad4 ASJ exome

AF:

0.0935

Gnomad4 EAS exome

AF:

0.0586

Gnomad4 SAS exome

AF:

0.0956

Gnomad4 FIN exome

AF:

0.0407

Gnomad4 NFE exome

AF:

0.0641

Gnomad4 OTH exome

AF:

0.0711

GnomAD4 genome

AF:

0.0831

AC:

12642

AN:

152128

Hom.:

644

Cov.:

AF XY:

0.0813

AC XY:

6049

AN XY:

74368

show subpopulations

Gnomad4 AFR

AF:

0.141

Gnomad4 AMR

AF:

0.0501

Gnomad4 ASJ

AF:

0.0948

Gnomad4 EAS

AF:

0.0486

Gnomad4 SAS

AF:

0.100

Gnomad4 FIN

AF:

0.0400

Gnomad4 NFE

AF:

0.0631

Gnomad4 OTH

AF:

0.0752

Alfa

AF:

0.0689

Hom.:

561

Bravo

AF:

0.0864

Asia WGS

AF:

0.0740

AC:

258

AN:

3478

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	May 10, 2021	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.19

CADD

Benign

DANN

Benign

0.91

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