rs756031843
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Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 2P and 11B. PM2BP4_StrongBP6_ModerateBP7BS1
The NM_005076.5(CNTN2):āc.2163T>Cā(p.Gly721=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000868 in 1,613,688 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ).
Frequency
Genomes: š 0.0000066 ( 0 hom., cov: 32)
Exomes š: 0.0000089 ( 0 hom. )
Consequence
CNTN2
NM_005076.5 synonymous
NM_005076.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.390
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 -9 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.8).
BP6
?
Variant 1-205069528-T-C is Benign according to our data. Variant chr1-205069528-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 541415.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-0.39 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population amr. gnomad4_exome allele frequency = 0.00000889 (13/1461724) while in subpopulation AMR AF= 0.000291 (13/44718). AF 95% confidence interval is 0.000171. There are 0 homozygotes in gnomad4_exome. There are 6 alleles in male gnomad4_exome subpopulation. Median coverage is 30. This position pass quality control queck.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CNTN2 | NM_005076.5 | c.2163T>C | p.Gly721= | synonymous_variant | 17/23 | ENST00000331830.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CNTN2 | ENST00000331830.7 | c.2163T>C | p.Gly721= | synonymous_variant | 17/23 | 1 | NM_005076.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000658 AC: 1AN: 151964Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000523 AC: 13AN: 248546Hom.: 0 AF XY: 0.0000446 AC XY: 6AN XY: 134570
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GnomAD4 exome AF: 0.00000889 AC: 13AN: 1461724Hom.: 0 Cov.: 30 AF XY: 0.00000825 AC XY: 6AN XY: 727164
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GnomAD4 genome ? AF: 0.00000658 AC: 1AN: 151964Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74222
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Epilepsy, familial adult myoclonic, 5 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jun 18, 2023 | - - |
Computational scores
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Name
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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