GeneBe

rs67417831

Variant names:

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_001040142.2(SCN2A):​c.-51-1752_-51-1735delAAAAAAAAAAAAAAAAAA variant causes a intron change involving the alteration of a non-conserved nucleotide. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 0)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

SCN2A
NM_001040142.2 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.78

Publications

0 publications found
Variant links:
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 disorder
    Inheritance: AD Classification: DEFINITIVE Submitted by: ClinGen, Illumina
  • developmental and epileptic encephalopathy, 11
    Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: G2P, Ambry Genetics, Labcorp Genetics (formerly Invitae)
  • intellectual disability
    Inheritance: AD Classification: DEFINITIVE Submitted by: G2P
  • episodic ataxia, type 9
    Inheritance: AD Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)
  • seizures, benign familial infantile, 3
    Inheritance: AD Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics
  • benign familial infantile epilepsy
    Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
  • benign familial neonatal-infantile seizures
    Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
  • Dravet syndrome
    Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
  • genetic developmental and epileptic encephalopathy
    Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
  • infantile spasms
    Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
  • malignant migrating partial seizures of infancy
    Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
SCN2ANM_001040142.2 linkc.-51-1752_-51-1735delAAAAAAAAAAAAAAAAAA intron_variant Intron 1 of 26 ENST00000375437.7 NP_001035232.1 Q99250-1
SCN2ANM_001371246.1 linkc.-51-1752_-51-1735delAAAAAAAAAAAAAAAAAA intron_variant Intron 1 of 26 ENST00000631182.3 NP_001358175.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SCN2AENST00000375437.7 linkc.-51-1762_-51-1745delAAAAAAAAAAAAAAAAAA intron_variant Intron 1 of 26 5 NM_001040142.2 ENSP00000364586.2 Q99250-1
SCN2AENST00000631182.3 linkc.-51-1762_-51-1745delAAAAAAAAAAAAAAAAAA intron_variant Intron 1 of 26 5 NM_001371246.1 ENSP00000486885.1 Q99250-2
SCN2AENST00000424833.5 linkc.-51-1762_-51-1745delAAAAAAAAAAAAAAAAAA intron_variant Intron 1 of 10 1 ENSP00000406454.2 F6U291
SCN2AENST00000283256.10 linkc.-176_-159delAAAAAAAAAAAAAAAAAA upstream_gene_variant 1 ENSP00000283256.6 Q99250-1

Frequencies

GnomAD3 genomes
Cov.:
0
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
0.00
AC:
0
AN:
95118
Hom.:
0
AF XY:
0.00
AC XY:
0
AN XY:
45646
African (AFR)
AF:
0.00
AC:
0
AN:
2706
American (AMR)
AF:
0.00
AC:
0
AN:
160
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
748
East Asian (EAS)
AF:
0.00
AC:
0
AN:
444
South Asian (SAS)
AF:
0.00
AC:
0
AN:
2156
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
42
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
238
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
85204
Other (OTH)
AF:
0.00
AC:
0
AN:
3420
GnomAD4 genome
Cov.:
0
Alfa
AF:
0.00
Hom.:
0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
PhyloP100
2.8

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs67417831; hg19: chr2-166150520; API