dbSNP rs2291101: CNTN6:p.Val753Val (chr3-1383034-G-A) – ACMG Classification: Benign (-21 pts)

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_001289080.2(CNTN6):c.2259G>A(p.Val753Val) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.435 in 1,613,376 control chromosomes in the GnomAD database, including 155,730 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.42 ( 13691 hom., cov: 32)

Exomes 𝑓: 0.44 ( 142039 hom. )

Consequence

CNTN6
NM_001289080.2 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: -1.27

Variant links:

Genes affected

CNTN6 (HGNC:2176): (contactin 6) The protein encoded by this gene is a member of the immunoglobulin superfamily. It is a glycosylphosphatidylinositol (GPI)-anchored neuronal membrane protein that functions as a cell adhesion molecule. It may play a role in the formation of axon connections in the developing nervous system. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2014]

CNTN6 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.76).

BP6

Variant 3-1383034-G-A is Benign according to our data. Variant chr3-1383034-G-A is described in ClinVar as [Benign]. Clinvar id is 402550.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-1.27 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.623 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CNTN6	NM_001289080.2 link	c.2259G>A	p.Val753Val	synonymous_variant	Exon 18 of 23	ENST00000446702.7	NP_001276009.1	Q9UQ52A1LMA8B4DGV0

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	UniProt
CNTN6	ENST00000446702.7 link	c.2259G>A	p.Val753Val	synonymous_variant	Exon 18 of 23	1	NM_001289080.2	ENSP00000407822.2	Q9UQ52
CNTN6	ENST00000350110.2 link	c.2259G>A	p.Val753Val	synonymous_variant	Exon 18 of 23	1		ENSP00000341882.2	Q9UQ52
CNTN6	ENST00000397479.6 link	n.*2397G>A		non_coding_transcript_exon_variant	Exon 17 of 22	2		ENSP00000380616.2	F8VWS7
CNTN6	ENST00000397479.6 link	n.*2397G>A		3_prime_UTR_variant	Exon 17 of 22	2		ENSP00000380616.2	F8VWS7

Frequencies

GnomAD3 genomes

AF:

0.418

AC:

63444

AN:

151888

Hom.:

13675

Cov.:

show subpopulations

Gnomad AFR

AF:

0.374

Gnomad AMI

AF:

0.448

Gnomad AMR

AF:

0.502

Gnomad ASJ

AF:

0.414

Gnomad EAS

AF:

0.641

Gnomad SAS

AF:

0.517

Gnomad FIN

AF:

0.291

Gnomad MID

AF:

0.408

Gnomad NFE

AF:

0.421

Gnomad OTH

AF:

0.418

GnomAD3 exomes

AF:

0.450

AC:

113114

AN:

251386

Hom.:

26586

AF XY:

0.450

AC XY:

61121

AN XY:

135874

show subpopulations

Gnomad AFR exome

AF:

0.373

Gnomad AMR exome

AF:

0.536

Gnomad ASJ exome

AF:

0.403

Gnomad EAS exome

AF:

0.641

Gnomad SAS exome

AF:

0.520

Gnomad FIN exome

AF:

0.301

Gnomad NFE exome

AF:

0.418

Gnomad OTH exome

AF:

0.433

GnomAD4 exome

AF:

0.437

AC:

638619

AN:

1461370

Hom.:

142039

Cov.:

AF XY:

0.438

AC XY:

318707

AN XY:

727024

show subpopulations

Gnomad4 AFR exome

AF:

0.368

Gnomad4 AMR exome

AF:

0.535

Gnomad4 ASJ exome

AF:

0.402

Gnomad4 EAS exome

AF:

0.627

Gnomad4 SAS exome

AF:

0.521

Gnomad4 FIN exome

AF:

0.302

Gnomad4 NFE exome

AF:

0.428

Gnomad4 OTH exome

AF:

0.444

GnomAD4 genome

AF:

0.418

AC:

63511

AN:

152006

Hom.:

13691

Cov.:

AF XY:

0.418

AC XY:

31042

AN XY:

74286

show subpopulations

Gnomad4 AFR

AF:

0.375

Gnomad4 AMR

AF:

0.502

Gnomad4 ASJ

AF:

0.414

Gnomad4 EAS

AF:

0.641

Gnomad4 SAS

AF:

0.518

Gnomad4 FIN

AF:

0.291

Gnomad4 NFE

AF:

0.421

Gnomad4 OTH

AF:

0.418

Alfa

AF:

0.415

Hom.:

7340

Bravo

AF:

0.429

Asia WGS

AF:

0.548

AC:

1900

AN:

3478

EpiCase

AF:

0.426

EpiControl

AF:

0.431

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:1

Mar 29, 2016

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency -

not provided

Benign:1

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.76

CADD

Benign

0.36

DANN

Benign

0.60

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