Variant 3-86065684-G-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_001167675.2(CADM2):c.1050G>C(p.Thr350Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00777 in 1,613,940 control chromosomes in the GnomAD database, including 66 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0055 ( 5 hom., cov: 32)

Exomes 𝑓: 0.0080 ( 61 hom. )

Consequence

CADM2
NM_001167675.2 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -3.07

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 -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.51).

BP6

Variant 3-86065684-G-C is Benign according to our data. Variant chr3-86065684-G-C is described in ClinVar as [Benign]. Clinvar id is 788972.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-3.07 with no splicing effect.

BS2

High AC in GnomAd4 at 842 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CADM2	NM_001167675.2 linkuse as main transcript	c.1050G>C	p.Thr350Thr	synonymous_variant	9/10	ENST00000383699.8	NP_001161147.1	Q8N3J6-2G3XHN4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
CADM2	ENST00000383699.8 linkuse as main transcript	c.1050G>C	p.Thr350Thr	synonymous_variant	9/10	1	NM_001167675.2	ENSP00000373200.3	Q8N3J6-2
CADM2	ENST00000405615.2 linkuse as main transcript	c.1149G>C	p.Thr383Thr	synonymous_variant	9/10	1		ENSP00000384193.2	Q8N3J6-3
CADM2	ENST00000407528.6 linkuse as main transcript	c.1143G>C	p.Thr381Thr	synonymous_variant	9/10	1		ENSP00000384575.2	Q8N3J6-1

Frequencies

GnomAD3 genomes

AF:

0.00554

AC:

843

AN:

152174

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00157

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00543

Gnomad ASJ

AF:

0.0187

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00558

Gnomad FIN

AF:

0.000566

Gnomad MID

AF:

0.00637

Gnomad NFE

AF:

0.00850

Gnomad OTH

AF:

0.00812

GnomAD3 exomes

AF:

0.00570

AC:

1432

AN:

251132

Hom.:

AF XY:

0.00607

AC XY:

824

AN XY:

135734

show subpopulations

Gnomad AFR exome

AF:

0.00154

Gnomad AMR exome

AF:

0.00512

Gnomad ASJ exome

AF:

0.0168

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00526

Gnomad FIN exome

AF:

0.000370

Gnomad NFE exome

AF:

0.00753

Gnomad OTH exome

AF:

0.00605

GnomAD4 exome

AF:

0.00800

AC:

11697

AN:

1461648

Hom.:

Cov.:

AF XY:

0.00791

AC XY:

5752

AN XY:

727124

show subpopulations

Gnomad4 AFR exome

AF:

0.000926

Gnomad4 AMR exome

AF:

0.00512

Gnomad4 ASJ exome

AF:

0.0157

Gnomad4 EAS exome

AF:

0.0000252

Gnomad4 SAS exome

AF:

0.00535

Gnomad4 FIN exome

AF:

0.000524

Gnomad4 NFE exome

AF:

0.00908

Gnomad4 OTH exome

AF:

0.00712

GnomAD4 genome

AF:

0.00553

AC:

842

AN:

152292

Hom.:

Cov.:

AF XY:

0.00471

AC XY:

351

AN XY:

74454

show subpopulations

Gnomad4 AFR

AF:

0.00156

Gnomad4 AMR

AF:

0.00542

Gnomad4 ASJ

AF:

0.0187

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00538

Gnomad4 FIN

AF:

0.000566

Gnomad4 NFE

AF:

0.00850

Gnomad4 OTH

AF:

0.00803

Alfa

AF:

0.00621

Hom.:

Bravo

AF:

0.00569

Asia WGS

AF:

0.00231

AC:

AN:

3478

EpiCase

AF:

0.00862

EpiControl

AF:

0.00730

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

May 24, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.51

CADD

Benign

0.11

DANN

Benign

0.70

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