2-165294010-TAAAAAAAAAA-T
Variant summary
Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1
The NM_001040142.2(SCN2A):c.-51-1744_-51-1735delAAAAAAAAAA variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.0050 ( 8 hom., cov: 0)
Exomes 𝑓: 0.00090 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
SCN2A
NM_001040142.2 intron
NM_001040142.2 intron
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 2.78
Publications
0 publications found
Genes affected
SCN2A (HGNC:10588): (sodium voltage-gated channel alpha subunit 2) Voltage-gated sodium channels are transmembrane glycoprotein complexes composed of a large alpha subunit with four repeat domains, each of which is composed of six membrane-spanning segments, and one or more regulatory beta subunits. Voltage-gated sodium channels function in the generation and propagation of action potentials in neurons and muscle. This gene encodes one member of the sodium channel alpha subunit gene family. Allelic variants of this gene are associated with seizure disorders and autism spectrum disorder. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Nov 2016]
SCN2A Gene-Disease associations (from GenCC):
- complex neurodevelopmental disorderInheritance: AD Classification: DEFINITIVE Submitted by: ClinGen, Illumina
- developmental and epileptic encephalopathy, 11Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: G2P, Ambry Genetics, Labcorp Genetics (formerly Invitae)
- intellectual disabilityInheritance: AD Classification: DEFINITIVE Submitted by: G2P
- episodic ataxia, type 9Inheritance: AD Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)
- seizures, benign familial infantile, 3Inheritance: AD Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics
- benign familial infantile epilepsyInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
- benign familial neonatal-infantile seizuresInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
- Dravet syndromeInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
- genetic developmental and epileptic encephalopathyInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
- infantile spasmsInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
- malignant migrating partial seizures of infancyInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
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ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -8 ACMG points.
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0511 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SCN2A | NM_001040142.2 | c.-51-1744_-51-1735delAAAAAAAAAA | intron_variant | Intron 1 of 26 | ENST00000375437.7 | NP_001035232.1 | ||
SCN2A | NM_001371246.1 | c.-51-1744_-51-1735delAAAAAAAAAA | intron_variant | Intron 1 of 26 | ENST00000631182.3 | NP_001358175.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SCN2A | ENST00000375437.7 | c.-51-1762_-51-1753delAAAAAAAAAA | intron_variant | Intron 1 of 26 | 5 | NM_001040142.2 | ENSP00000364586.2 | |||
SCN2A | ENST00000631182.3 | c.-51-1762_-51-1753delAAAAAAAAAA | intron_variant | Intron 1 of 26 | 5 | NM_001371246.1 | ENSP00000486885.1 | |||
SCN2A | ENST00000424833.5 | c.-51-1762_-51-1753delAAAAAAAAAA | intron_variant | Intron 1 of 10 | 1 | ENSP00000406454.2 | ||||
SCN2A | ENST00000283256.10 | c.-176_-167delAAAAAAAAAA | upstream_gene_variant | 1 | ENSP00000283256.6 |
Frequencies
GnomAD3 genomes AF: 0.00501 AC: 280AN: 55932Hom.: 8 Cov.: 0 show subpopulations
GnomAD3 genomes
AF:
AC:
280
AN:
55932
Hom.:
Cov.:
0
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:
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.000904 AC: 86AN: 95122Hom.: 0 AF XY: 0.000635 AC XY: 29AN XY: 45646 show subpopulations
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
AF:
AC:
86
AN:
95122
Hom.:
AF XY:
AC XY:
29
AN XY:
45646
show subpopulations
African (AFR)
AF:
AC:
2
AN:
2706
American (AMR)
AF:
AC:
20
AN:
160
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
748
East Asian (EAS)
AF:
AC:
15
AN:
444
South Asian (SAS)
AF:
AC:
2
AN:
2158
European-Finnish (FIN)
AF:
AC:
0
AN:
42
Middle Eastern (MID)
AF:
AC:
0
AN:
238
European-Non Finnish (NFE)
AF:
AC:
22
AN:
85206
Other (OTH)
AF:
AC:
25
AN:
3420
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.531
Heterozygous variant carriers
0
3
6
9
12
15
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome AF: 0.00501 AC: 280AN: 55942Hom.: 8 Cov.: 0 AF XY: 0.00579 AC XY: 141AN XY: 24338 show subpopulations
GnomAD4 genome
AF:
AC:
280
AN:
55942
Hom.:
Cov.:
0
AF XY:
AC XY:
141
AN XY:
24338
show subpopulations
African (AFR)
AF:
AC:
31
AN:
13604
American (AMR)
AF:
AC:
195
AN:
3380
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
1982
East Asian (EAS)
AF:
AC:
33
AN:
1508
South Asian (SAS)
AF:
AC:
2
AN:
864
European-Finnish (FIN)
AF:
AC:
0
AN:
298
Middle Eastern (MID)
AF:
AC:
1
AN:
46
European-Non Finnish (NFE)
AF:
AC:
9
AN:
33120
Other (OTH)
AF:
AC:
9
AN:
636
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.568
Heterozygous variant carriers
0
10
19
29
38
48
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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