rs566959580
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Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2
The ENST00000331830.7(CNTN2):c.2964G>A(p.Gly988=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000773 in 1,614,116 control chromosomes in the GnomAD database, including 22 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.00053 ( 1 hom., cov: 32)
Exomes 𝑓: 0.00080 ( 21 hom. )
Consequence
CNTN2
ENST00000331830.7 synonymous
ENST00000331830.7 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.541
Genes affected
CNTN2 (HGNC:2172): (contactin 2) This gene encodes a member of the contactin family of proteins, part of the immunoglobulin superfamily of cell adhesion molecules. The encoded glycosylphosphatidylinositol (GPI)-anchored neuronal membrane protein plays a role in the proliferation, migration, and axon guidance of neurons of the developing cerebellum. A mutation in this gene may be associated with adult myoclonic epilepsy. [provided by RefSeq, Sep 2016]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -15 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.54).
BP6
Variant 1-205073187-G-A is Benign according to our data. Variant chr1-205073187-G-A is described in ClinVar as [Benign]. Clinvar id is 541416.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-0.541 with no splicing effect.
BS1
Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.000525 (80/152272) while in subpopulation SAS AF= 0.016 (77/4824). AF 95% confidence interval is 0.0131. There are 1 homozygotes in gnomad4. There are 51 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High Homozygotes in GnomAdExome4 at 21 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CNTN2 | NM_005076.5 | c.2964G>A | p.Gly988= | synonymous_variant | 22/23 | ENST00000331830.7 | NP_005067.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CNTN2 | ENST00000331830.7 | c.2964G>A | p.Gly988= | synonymous_variant | 22/23 | 1 | NM_005076.5 | ENSP00000330633 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000526 AC: 80AN: 152154Hom.: 1 Cov.: 32
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GnomAD3 exomes AF: 0.00168 AC: 421AN: 251082Hom.: 7 AF XY: 0.00230 AC XY: 312AN XY: 135752
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GnomAD4 exome AF: 0.000799 AC: 1168AN: 1461844Hom.: 21 Cov.: 31 AF XY: 0.00116 AC XY: 843AN XY: 727230
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GnomAD4 genome AF: 0.000525 AC: 80AN: 152272Hom.: 1 Cov.: 32 AF XY: 0.000685 AC XY: 51AN XY: 74462
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
CNTN2-related disorder Benign:1
Benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Feb 11, 2021 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Epilepsy, familial adult myoclonic, 5 Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 19, 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