Variant rs10784981 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001843.4(CNTN1):c.1805-14C>A variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.119 in 1,611,240 control chromosomes in the GnomAD database, including 11,974 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.12 ( 1087 hom., cov: 32)

Exomes 𝑓: 0.12 ( 10887 hom. )

Consequence

CNTN1
NM_001843.4 splice_polypyrimidine_tract, intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: -0.289

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 -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.78).

BP6

Variant 12-40980895-C-A is Benign according to our data. Variant chr12-40980895-C-A is described in ClinVar as [Benign]. Clinvar id is 258193.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr12-40980895-C-A is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.121 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.1805-14C>A		splice_polypyrimidine_tract_variant, intron_variant		ENST00000551295.7	NP_001834.2

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	Appris	UniProt
CNTN1	ENST00000551295.7 linkuse as main transcript	c.1805-14C>A	splice_polypyrimidine_tract_variant, intron_variant	1	NM_001843.4	ENSP00000447006	P3	Q12860-1
CNTN1	ENST00000347616.5 linkuse as main transcript	c.1805-14C>A	splice_polypyrimidine_tract_variant, intron_variant	1		ENSP00000325660	P3	Q12860-1
CNTN1	ENST00000348761.2 linkuse as main transcript	c.1772-14C>A	splice_polypyrimidine_tract_variant, intron_variant	1		ENSP00000261160	A1	Q12860-2

Frequencies

GnomAD3 genomes

AF:

0.117

AC:

17833

AN:

152078

Hom.:

1087

Cov.:

show subpopulations

Gnomad AFR

AF:

0.110

Gnomad AMI

AF:

0.0987

Gnomad AMR

AF:

0.116

Gnomad ASJ

AF:

0.147

Gnomad EAS

AF:

0.0629

Gnomad SAS

AF:

0.0726

Gnomad FIN

AF:

0.155

Gnomad MID

AF:

0.0854

Gnomad NFE

AF:

0.123

Gnomad OTH

AF:

0.112

GnomAD3 exomes

AF:

0.111

AC:

27869

AN:

250562

Hom.:

1682

AF XY:

0.111

AC XY:

15056

AN XY:

135430

show subpopulations

Gnomad AFR exome

AF:

0.107

Gnomad AMR exome

AF:

0.104

Gnomad ASJ exome

AF:

0.140

Gnomad EAS exome

AF:

0.0651

Gnomad SAS exome

AF:

0.0746

Gnomad FIN exome

AF:

0.153

Gnomad NFE exome

AF:

0.121

Gnomad OTH exome

AF:

0.117

GnomAD4 exome

AF:

0.119

AC:

174091

AN:

1459044

Hom.:

10887

Cov.:

AF XY:

0.118

AC XY:

85710

AN XY:

726006

show subpopulations

Gnomad4 AFR exome

AF:

0.109

Gnomad4 AMR exome

AF:

0.104

Gnomad4 ASJ exome

AF:

0.137

Gnomad4 EAS exome

AF:

0.0517

Gnomad4 SAS exome

AF:

0.0766

Gnomad4 FIN exome

AF:

0.149

Gnomad4 NFE exome

AF:

0.124

Gnomad4 OTH exome

AF:

0.118

GnomAD4 genome

AF:

0.117

AC:

17839

AN:

152196

Hom.:

1087

Cov.:

AF XY:

0.117

AC XY:

8687

AN XY:

74422

show subpopulations

Gnomad4 AFR

AF:

0.110

Gnomad4 AMR

AF:

0.116

Gnomad4 ASJ

AF:

0.147

Gnomad4 EAS

AF:

0.0624

Gnomad4 SAS

AF:

0.0729

Gnomad4 FIN

AF:

0.155

Gnomad4 NFE

AF:

0.123

Gnomad4 OTH

AF:

0.110

Alfa

AF:

0.0672

Hom.:

114

Bravo

AF:

0.116

Asia WGS

AF:

0.0780

AC:

270

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Feb 08, 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. -
Benign, criteria provided, single submitter	clinical testing	PreventionGenetics, part of Exact Sciences	-	- -

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

-0.78

CADD

Benign

3.7

DANN

Benign

0.59

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