2-165994210-G-A
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7
The NM_001165963.4(SCN1A):c.4788C>T(p.Arg1596=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000248 in 1,612,444 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. R1596R) has been classified as Likely benign.
Frequency
Consequence
NM_001165963.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SCN1A | NM_001165963.4 | c.4788C>T | p.Arg1596= | synonymous_variant | 28/29 | ENST00000674923.1 | |
LOC102724058 | NR_110598.1 | n.176-21403G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SCN1A | ENST00000674923.1 | c.4788C>T | p.Arg1596= | synonymous_variant | 28/29 | NM_001165963.4 | P4 | ||
SCN1A-AS1 | ENST00000651574.1 | n.193-21403G>A | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 151902Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 250144Hom.: 0 AF XY: 0.0000222 AC XY: 3AN XY: 135232
GnomAD4 exome AF: 0.00000205 AC: 3AN: 1460542Hom.: 0 Cov.: 31 AF XY: 0.00000275 AC XY: 2AN XY: 726598
GnomAD4 genome AF: 0.00000658 AC: 1AN: 151902Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74172
ClinVar
Submissions by phenotype
Early infantile epileptic encephalopathy with suppression bursts Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Apr 15, 2017 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at