Variant 3-85886263-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_ModerateBP6_Very_StrongBP7BS2

The ENST00000383699.8(CADM2):c.465C>T(p.Cys155=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00529 in 1,613,660 control chromosomes in the GnomAD database, including 23 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0038 ( 1 hom., cov: 32)

Exomes 𝑓: 0.0054 ( 22 hom. )

Consequence

CADM2
ENST00000383699.8 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: 0.473

Variant links:

Genes affected

CADM2 (HGNC:29849): (cell adhesion molecule 2) This gene encodes a member of the synaptic cell adhesion molecule 1 (SynCAM) family which belongs to the immunoglobulin (Ig) superfamily. The encoded protein has three Ig-like domains and a cytosolic protein 4.1 binding site near the C-terminus. Proteins belonging to the protein 4.1 family crosslink spectrin and interact with other cytoskeletal proteins. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Feb 2012]

CADM2 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4

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

BP6

Variant 3-85886263-C-T is Benign according to our data. Variant chr3-85886263-C-T is described in ClinVar as [Benign]. Clinvar id is 783311.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=0.473 with no splicing effect.

BS2

High AC in GnomAd4 at 573 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CADM2	NM_001167675.2 linkuse as main transcript	c.465C>T	p.Cys155=	synonymous_variant	5/10	ENST00000383699.8	NP_001161147.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CADM2	ENST00000383699.8 linkuse as main transcript	c.465C>T	p.Cys155=	synonymous_variant	5/10	1	NM_001167675.2	ENSP00000373200	A1	Q8N3J6-2
CADM2	ENST00000405615.2 linkuse as main transcript	c.444C>T	p.Cys148=	synonymous_variant	4/10	1		ENSP00000384193		Q8N3J6-3
CADM2	ENST00000407528.6 linkuse as main transcript	c.438C>T	p.Cys146=	synonymous_variant	4/10	1		ENSP00000384575	P4	Q8N3J6-1

Frequencies

GnomAD3 genomes

AF:

0.00377

AC:

573

AN:

151982

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000967

Gnomad AMI

AF:

0.00110

Gnomad AMR

AF:

0.00144

Gnomad ASJ

AF:

0.00202

Gnomad EAS

AF:

0.000193

Gnomad SAS

AF:

0.000415

Gnomad FIN

AF:

0.000852

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.00695

Gnomad OTH

AF:

0.00766

GnomAD3 exomes

AF:

0.00384

AC:

964

AN:

251172

Hom.:

AF XY:

0.00376

AC XY:

510

AN XY:

135744

show subpopulations

Gnomad AFR exome

AF:

0.000677

Gnomad AMR exome

AF:

0.00202

Gnomad ASJ exome

AF:

0.000894

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000196

Gnomad FIN exome

AF:

0.00111

Gnomad NFE exome

AF:

0.00721

Gnomad OTH exome

AF:

0.00425

GnomAD4 exome

AF:

0.00545

AC:

7961

AN:

1461558

Hom.:

Cov.:

AF XY:

0.00516

AC XY:

3752

AN XY:

727072

show subpopulations

Gnomad4 AFR exome

AF:

0.00105

Gnomad4 AMR exome

AF:

0.00221

Gnomad4 ASJ exome

AF:

0.000842

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.000278

Gnomad4 FIN exome

AF:

0.00120

Gnomad4 NFE exome

AF:

0.00667

Gnomad4 OTH exome

AF:

0.00459

GnomAD4 genome

AF:

0.00377

AC:

573

AN:

152102

Hom.:

Cov.:

AF XY:

0.00346

AC XY:

257

AN XY:

74340

show subpopulations

Gnomad4 AFR

AF:

0.000964

Gnomad4 AMR

AF:

0.00144

Gnomad4 ASJ

AF:

0.00202

Gnomad4 EAS

AF:

0.000194

Gnomad4 SAS

AF:

0.000415

Gnomad4 FIN

AF:

0.000852

Gnomad4 NFE

AF:

0.00695

Gnomad4 OTH

AF:

0.00758

Alfa

AF:

0.00558

Hom.:

Bravo

AF:

0.00388

EpiCase

AF:

0.00688

EpiControl

AF:

0.00593

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	Labcorp Genetics (formerly Invitae), Labcorp	Jul 31, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.39

CADD

Benign

5.9

DANN

Benign

0.47

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