Variant rs935105 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_001843.4(CNTN1):c.1014T>C(p.Asn338=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.123 in 1,612,934 control chromosomes in the GnomAD database, including 12,701 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.13 ( 1453 hom., cov: 32)

Exomes 𝑓: 0.12 ( 11248 hom. )

Consequence

CNTN1
NM_001843.4 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:5

Conservation

PhyloP100: 0.171

Variant links:

Genes affected

CNTN1 (HGNC:2171): (contactin 1) 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. Multiple alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2011]

CNTN1 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=-0.5).

BP6

Variant 12-40936809-T-C is Benign according to our data. Variant chr12-40936809-T-C is described in ClinVar as [Benign]. Clinvar id is 128790.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr12-40936809-T-C is described in Lovd as [Benign].

BP7

Synonymous conserved (PhyloP=0.171 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.168 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CNTN1	NM_001843.4 linkuse as main transcript	c.1014T>C	p.Asn338=	synonymous_variant	10/24	ENST00000551295.7	NP_001834.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CNTN1	ENST00000551295.7 linkuse as main transcript	c.1014T>C	p.Asn338=	synonymous_variant	10/24	1	NM_001843.4	ENSP00000447006	P3	Q12860-1

Frequencies

GnomAD3 genomes

AF:

0.135

AC:

20497

AN:

152042

Hom.:

1454

Cov.:

show subpopulations

Gnomad AFR

AF:

0.171

Gnomad AMI

AF:

0.0989

Gnomad AMR

AF:

0.122

Gnomad ASJ

AF:

0.146

Gnomad EAS

AF:

0.0628

Gnomad SAS

AF:

0.0731

Gnomad FIN

AF:

0.154

Gnomad MID

AF:

0.0886

Gnomad NFE

AF:

0.123

Gnomad OTH

AF:

0.129

GnomAD3 exomes

AF:

0.116

AC:

29040

AN:

250680

Hom.:

1842

AF XY:

0.114

AC XY:

15491

AN XY:

135436

show subpopulations

Gnomad AFR exome

AF:

0.169

Gnomad AMR exome

AF:

0.107

Gnomad ASJ exome

AF:

0.140

Gnomad EAS exome

AF:

0.0655

Gnomad SAS exome

AF:

0.0743

Gnomad FIN exome

AF:

0.153

Gnomad NFE exome

AF:

0.121

Gnomad OTH exome

AF:

0.120

GnomAD4 exome

AF:

0.121

AC:

177446

AN:

1460774

Hom.:

11248

Cov.:

AF XY:

0.120

AC XY:

87103

AN XY:

726676

show subpopulations

Gnomad4 AFR exome

AF:

0.171

Gnomad4 AMR exome

AF:

0.107

Gnomad4 ASJ exome

AF:

0.138

Gnomad4 EAS exome

AF:

0.0515

Gnomad4 SAS exome

AF:

0.0763

Gnomad4 FIN exome

AF:

0.149

Gnomad4 NFE exome

AF:

0.125

Gnomad4 OTH exome

AF:

0.122

GnomAD4 genome

AF:

0.135

AC:

20512

AN:

152160

Hom.:

1453

Cov.:

AF XY:

0.134

AC XY:

9994

AN XY:

74400

show subpopulations

Gnomad4 AFR

AF:

0.171

Gnomad4 AMR

AF:

0.122

Gnomad4 ASJ

AF:

0.146

Gnomad4 EAS

AF:

0.0624

Gnomad4 SAS

AF:

0.0734

Gnomad4 FIN

AF:

0.154

Gnomad4 NFE

AF:

0.123

Gnomad4 OTH

AF:

0.127

Alfa

AF:

0.127

Hom.:

886

Bravo

AF:

0.136

Asia WGS

AF:

0.0810

AC:

281

AN:

3478

EpiCase

AF:

0.120

EpiControl

AF:

0.122

ClinVar

Significance: Benign

Submissions summary: Benign:5

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:3

Benign, criteria provided, single submitter	clinical testing	PreventionGenetics, part of Exact Sciences	-	- -
Benign, criteria provided, single submitter	clinical testing	Genetic Services Laboratory, University of Chicago	Aug 15, 2013	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jan 26, 2016	This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

not provided

Benign:1

Benign, criteria provided, single submitter

not provided

Breakthrough Genomics, Breakthrough Genomics

- -

Compton-North congenital myopathy

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jan 31, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.50

CADD

Benign

5.9

DANN

Benign

0.65

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