rs1056019
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Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_001843.4(CNTN1):c.1416C>T(p.Asn472=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.618 in 1,591,976 control chromosomes in the GnomAD database, including 305,935 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.62 ( 29423 hom., cov: 32)
Exomes 𝑓: 0.62 ( 276512 hom. )
Consequence
CNTN1
NM_001843.4 synonymous
NM_001843.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.557
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -21 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.72).
BP6
?
Variant 12-40943633-C-T is Benign according to our data. Variant chr12-40943633-C-T is described in ClinVar as [Benign]. Clinvar id is 128791.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr12-40943633-C-T is described in Lovd as [Benign].
BP7
?
Synonymous conserved (PhyloP=-0.557 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.65 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CNTN1 | NM_001843.4 | c.1416C>T | p.Asn472= | synonymous_variant | 13/24 | ENST00000551295.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CNTN1 | ENST00000551295.7 | c.1416C>T | p.Asn472= | synonymous_variant | 13/24 | 1 | NM_001843.4 | P3 |
Frequencies
GnomAD3 genomes ? AF: 0.621 AC: 94288AN: 151734Hom.: 29414 Cov.: 32
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GnomAD3 exomes AF: 0.621 AC: 155177AN: 249942Hom.: 48729 AF XY: 0.618 AC XY: 83439AN XY: 135070
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GnomAD4 exome AF: 0.618 AC: 889684AN: 1440126Hom.: 276512 Cov.: 32 AF XY: 0.617 AC XY: 442770AN XY: 717712
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GnomAD4 genome ? AF: 0.621 AC: 94323AN: 151850Hom.: 29423 Cov.: 32 AF XY: 0.622 AC XY: 46118AN XY: 74174
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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 05, 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. - |
Compton-North congenital myopathy Benign:2
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 22, 2021 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at