rs9787172
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Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BA1
The NM_005076.5(CNTN2):c.297C>T(p.Asn99=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0351 in 1,548,416 control chromosomes in the GnomAD database, including 1,704 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.052 ( 328 hom., cov: 32)
Exomes 𝑓: 0.033 ( 1376 hom. )
Consequence
CNTN2
NM_005076.5 synonymous
NM_005076.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.06
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 -19 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.37).
BP6
?
Variant 1-205058262-C-T is Benign according to our data. Variant chr1-205058262-C-T is described in ClinVar as [Benign]. Clinvar id is 474482.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
?
Synonymous conserved (PhyloP=1.06 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.116 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CNTN2 | NM_005076.5 | c.297C>T | p.Asn99= | synonymous_variant | 4/23 | ENST00000331830.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CNTN2 | ENST00000331830.7 | c.297C>T | p.Asn99= | synonymous_variant | 4/23 | 1 | NM_005076.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0523 AC: 7959AN: 152070Hom.: 322 Cov.: 32
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GnomAD3 exomes AF: 0.0468 AC: 9240AN: 197604Hom.: 358 AF XY: 0.0489 AC XY: 5116AN XY: 104522
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GnomAD4 exome AF: 0.0332 AC: 46419AN: 1396228Hom.: 1376 Cov.: 32 AF XY: 0.0355 AC XY: 24375AN XY: 687328
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GnomAD4 genome ? AF: 0.0524 AC: 7981AN: 152188Hom.: 328 Cov.: 32 AF XY: 0.0554 AC XY: 4125AN XY: 74420
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Oct 15, 2018 | - - |
Epilepsy, familial adult myoclonic, 5 Benign:1
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