7-146116214-TGGCGGC-T
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1
The ENST00000625365.2(CNTNAP2):c.-230+126_-230+131delGGCGGC variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.994 in 151,762 control chromosomes in the GnomAD database, including 75,094 homozygotes. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 1.0 ( 74872 hom., cov: 0)
Exomes 𝑓: 0.80 ( 222 hom. )
Consequence
CNTNAP2
ENST00000625365.2 intron
ENST00000625365.2 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 1.69
Genes affected
CNTNAP2 (HGNC:13830): (contactin associated protein 2) This gene encodes a member of the neurexin family which functions in the vertebrate nervous system as cell adhesion molecules and receptors. This protein, like other neurexin proteins, contains epidermal growth factor repeats and laminin G domains. In addition, it includes an F5/8 type C domain, discoidin/neuropilin- and fibrinogen-like domains, thrombospondin N-terminal-like domains and a putative PDZ binding site. This protein is localized at the juxtaparanodes of myelinated axons, and mediates interactions between neurons and glia during nervous system development and is also involved in localization of potassium channels within differentiating axons. This gene encompasses almost 1.5% of chromosome 7 and is one of the largest genes in the human genome. It is directly bound and regulated by forkhead box protein P2, a transcription factor related to speech and language development. This gene has been implicated in multiple neurodevelopmental disorders, including Gilles de la Tourette syndrome, schizophrenia, epilepsy, autism, ADHD and intellectual disability. [provided by RefSeq, Jul 2017]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP6
Variant 7-146116214-TGGCGGC-T is Benign according to our data. Variant chr7-146116214-TGGCGGC-T is described in ClinVar as [Benign]. Clinvar id is 1263242.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.99 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
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Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CNTNAP2 | ENST00000625365.2 | c.-230+126_-230+131delGGCGGC | intron_variant | 5 | ENSP00000485955.1 |
Frequencies
GnomAD3 genomes AF: 0.995 AC: 150350AN: 151068Hom.: 74820 Cov.: 0
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GnomAD4 exome AF: 0.796 AC: 468AN: 588Hom.: 222 AF XY: 0.774 AC XY: 325AN XY: 420
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GnomAD4 genome AF: 0.995 AC: 150455AN: 151174Hom.: 74872 Cov.: 0 AF XY: 0.996 AC XY: 73522AN XY: 73852
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Aug 10, 2019 | - - |
Computational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at