rs6873671

Variant names:

• chr5-11137583-C-G
• rs6873671
• NM_001332.4:c.2160-20016G>C

Your query was ambiguous. Multiple possible variants found:

• chr5-11137583-C-G
• chr5-11137583-C-T

Variant summary

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

The NM_001332.4(CTNND2):​c.2160-20016G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.624 in 152,014 control chromosomes in the GnomAD database, including 29,651 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 0.62 (29651 hom., cov: 32)
• Consequence: CTNND2 NM_001332.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.232
• Publications: 6 publications found

Genes affected

CTNND2 (HGNC:2516): (catenin delta 2) This gene encodes an adhesive junction associated protein of the armadillo/beta-catenin superfamily and is implicated in brain and eye development and cancer formation. The protein encoded by this gene promotes the disruption of E-cadherin based adherens junction to favor cell spreading upon stimulation by hepatocyte growth factor. This gene is overexpressed in prostate adenocarcinomas and is associated with decreased expression of tumor suppressor E-cadherin in this tissue. This gene resides in a region of the short arm of chromosome 5 that is deleted in Cri du Chat syndrome. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Dec 2013]

CTNND2 Gene-Disease associations (from GenCC):

• complex neurodevelopmental disorder

  Inheritance: AD Classification: STRONG Submitted by: Illumina
• neurodevelopmental disorder

  Inheritance: AD Classification: STRONG Submitted by: G2P
• benign adult familial myoclonic epilepsy

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.715 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001332.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CTNND2	NM_001332.4	MANE Select	c.2160-20016G>C		intron	N/A	NP_001323.1
	CTNND2	NM_001288715.1		c.1887-20016G>C		intron	N/A	NP_001275644.1
	CTNND2	NM_001364128.2		c.1149-20016G>C		intron	N/A	NP_001351057.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CTNND2	ENST00000304623.13	TSL:1 MANE Select	c.2160-20016G>C		intron	N/A	ENSP00000307134.8
	CTNND2	ENST00000511377.5	TSL:1	c.1887-20016G>C		intron	N/A	ENSP00000426510.1
	CTNND2	ENST00000513588.5	TSL:1	n.1422-20016G>C		intron	N/A	ENSP00000421093.1

Frequencies

GnomAD3 genomes AF: 0.624 AC: 94766 AN: 151896 Hom.: 29613 Cov.: 32

Gnomad AFR AF: 0.609

Gnomad AMI AF: 0.731

Gnomad AMR AF: 0.656

Gnomad ASJ AF: 0.628

Gnomad EAS AF: 0.735

Gnomad SAS AF: 0.590

Gnomad FIN AF: 0.599

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.622

Gnomad OTH AF: 0.625

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

GnomAD4 genome AF: 0.624 AC: 94854 AN: 152014 Hom.: 29651 Cov.: 32 AF XY: 0.624 AC XY: 46398 AN XY: 74302

African (AFR) AF: 0.609 AC: 25282 AN: 41482

American (AMR) AF: 0.656 AC: 10008 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.628 AC: 2175 AN: 3464

East Asian (EAS) AF: 0.735 AC: 3790 AN: 5158

South Asian (SAS) AF: 0.591 AC: 2844 AN: 4814

European-Finnish (FIN) AF: 0.599 AC: 6312 AN: 10546

Middle Eastern (MID) AF: 0.558 AC: 164 AN: 294

European-Non Finnish (NFE) AF: 0.622 AC: 42293 AN: 67978

Other (OTH) AF: 0.627 AC: 1321 AN: 2108

Alfa AF: 0.624 Hom.: 3714

Bravo AF: 0.631

Asia WGS AF: 0.647 AC: 2250 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.1
DANN	Benign	0.50
PhyloP100		0.23
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: rs6873671; hg19: chr5-11137695;