rs61748365
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_001843.4(CNTN1):c.90T>C(p.His30=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0111 in 1,605,248 control chromosomes in the GnomAD database, including 149 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.0068 ( 14 hom., cov: 32)
Exomes 𝑓: 0.012 ( 135 hom. )
Consequence
CNTN1
NM_001843.4 synonymous
NM_001843.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 2.00
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=-0.5).
BP6
?
Variant 12-40910101-T-C is Benign according to our data. Variant chr12-40910101-T-C is described in ClinVar as [Benign]. Clinvar id is 258204.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
?
Synonymous conserved (PhyloP=2.01 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0068 (1035/152302) while in subpopulation NFE AF= 0.0125 (849/68006). AF 95% confidence interval is 0.0118. There are 14 homozygotes in gnomad4. There are 472 alleles in male gnomad4 subpopulation. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 14 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CNTN1 | NM_001843.4 | c.90T>C | p.His30= | synonymous_variant | 3/24 | ENST00000551295.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CNTN1 | ENST00000551295.7 | c.90T>C | p.His30= | synonymous_variant | 3/24 | 1 | NM_001843.4 | P3 |
Frequencies
GnomAD3 genomes ? AF: 0.00680 AC: 1035AN: 152184Hom.: 14 Cov.: 32
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GnomAD3 exomes AF: 0.00624 AC: 1565AN: 250910Hom.: 12 AF XY: 0.00657 AC XY: 891AN XY: 135658
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GnomAD4 exome AF: 0.0115 AC: 16741AN: 1452946Hom.: 135 Cov.: 27 AF XY: 0.0112 AC XY: 8127AN XY: 723418
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GnomAD4 genome ? AF: 0.00680 AC: 1035AN: 152302Hom.: 14 Cov.: 32 AF XY: 0.00634 AC XY: 472AN XY: 74478
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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:2
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 02, 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:2
Benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Mar 01, 2024 | CNTN1: BP4, BP7, BS1, BS2 - |
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Feb 27, 2019 | - - |
Compton-North congenital myopathy Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 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