rs759178
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_014141.6(CNTNAP2):c.2099-25545A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.57 in 152,018 control chromosomes in the GnomAD database, including 25,312 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.57 ( 25312 hom., cov: 32)
Consequence
CNTNAP2
NM_014141.6 intron
NM_014141.6 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.265
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]
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.687 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CNTNAP2 | NM_014141.6 | c.2099-25545A>C | intron_variant | Intron 13 of 23 | ENST00000361727.8 | NP_054860.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.570 AC: 86615AN: 151898Hom.: 25274 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
86615
AN:
151898
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.570 AC: 86702AN: 152018Hom.: 25312 Cov.: 32 AF XY: 0.567 AC XY: 42181AN XY: 74330 show subpopulations
GnomAD4 genome
AF:
AC:
86702
AN:
152018
Hom.:
Cov.:
32
AF XY:
AC XY:
42181
AN XY:
74330
Gnomad4 AFR
AF:
AC:
0.693828
AN:
0.693828
Gnomad4 AMR
AF:
AC:
0.585505
AN:
0.585505
Gnomad4 ASJ
AF:
AC:
0.609925
AN:
0.609925
Gnomad4 EAS
AF:
AC:
0.614032
AN:
0.614032
Gnomad4 SAS
AF:
AC:
0.484848
AN:
0.484848
Gnomad4 FIN
AF:
AC:
0.485138
AN:
0.485138
Gnomad4 NFE
AF:
AC:
0.507345
AN:
0.507345
Gnomad4 OTH
AF:
AC:
0.605138
AN:
0.605138
Heterozygous variant carriers
0
1890
3779
5669
7558
9448
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Genome Het
Genome Hom
Variant carriers
0
732
1464
2196
2928
3660
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
2026
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
Mutation Taster
=100/0
polymorphism (auto)
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at