rs10174400
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001040142.2(SCN2A):c.-51-27064C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.379 in 151,484 control chromosomes in the GnomAD database, including 11,292 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 0.38 ( 11292 hom., cov: 30)
Exomes 𝑓: 0.20 ( 0 hom. )
Consequence
SCN2A
NM_001040142.2 intron
NM_001040142.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.851
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-1.04).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.475 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SCN2A | NM_001040142.2 | c.-51-27064C>T | intron_variant | ENST00000375437.7 | |||
SCN2A | NM_001371246.1 | c.-51-27064C>T | intron_variant | ENST00000631182.3 | |||
SCN2A | NM_001040143.2 | c.-52+23261C>T | intron_variant | ||||
SCN2A | NM_001371247.1 | c.-51-27064C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SCN2A | ENST00000375437.7 | c.-51-27064C>T | intron_variant | 5 | NM_001040142.2 | P1 | |||
SCN2A | ENST00000631182.3 | c.-51-27064C>T | intron_variant | 5 | NM_001371246.1 |
Frequencies
GnomAD3 genomes ? AF: 0.379 AC: 57424AN: 151356Hom.: 11274 Cov.: 30
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GnomAD4 exome AF: 0.200 AC: 2AN: 10Hom.: 0 Cov.: 0 AF XY: 0.167 AC XY: 1AN XY: 6
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GnomAD4 genome ? AF: 0.380 AC: 57486AN: 151474Hom.: 11292 Cov.: 30 AF XY: 0.378 AC XY: 27945AN XY: 74014
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ClinVar
Not reported inComputational scores
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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