rs765041838
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_001040142.2(SCN2A):c.4656C>G(p.Thr1552=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000151 in 1,461,662 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. T1552T) has been classified as Likely benign.
Frequency
Consequence
NM_001040142.2 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SCN2A | NM_001040142.2 | c.4656C>G | p.Thr1552= | synonymous_variant | 26/27 | ENST00000375437.7 | |
SCN2A | NM_001371246.1 | c.4656C>G | p.Thr1552= | synonymous_variant | 26/27 | ENST00000631182.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SCN2A | ENST00000375437.7 | c.4656C>G | p.Thr1552= | synonymous_variant | 26/27 | 5 | NM_001040142.2 | P1 | |
SCN2A | ENST00000631182.3 | c.4656C>G | p.Thr1552= | synonymous_variant | 26/27 | 5 | NM_001371246.1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.0000199 AC: 5AN: 250874Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135564
GnomAD4 exome AF: 0.0000151 AC: 22AN: 1461662Hom.: 0 Cov.: 32 AF XY: 0.0000138 AC XY: 10AN XY: 727116
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
Seizures, benign familial infantile, 3;C3150987:Developmental and epileptic encephalopathy, 11 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jun 19, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at