rs564134251
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_ModerateBP6_Very_StrongBP7
The NM_000334.4(SCN4A):c.1947C>T(p.Ile649=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000403 in 1,613,970 control chromosomes in the GnomAD database, including 1 homozygotes. 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. I649I) has been classified as Likely benign.
Frequency
Consequence
NM_000334.4 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 |
---|---|---|---|---|---|---|---|
SCN4A | NM_000334.4 | c.1947C>T | p.Ile649= | synonymous_variant | 12/24 | ENST00000435607.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SCN4A | ENST00000435607.3 | c.1947C>T | p.Ile649= | synonymous_variant | 12/24 | 1 | NM_000334.4 | P1 | |
SCN4A | ENST00000581514.1 | downstream_gene_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000394 AC: 6AN: 152192Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000682 AC: 17AN: 249228Hom.: 0 AF XY: 0.0000961 AC XY: 13AN XY: 135206
GnomAD4 exome AF: 0.0000404 AC: 59AN: 1461660Hom.: 1 Cov.: 32 AF XY: 0.0000523 AC XY: 38AN XY: 727120
GnomAD4 genome ? AF: 0.0000394 AC: 6AN: 152310Hom.: 0 Cov.: 32 AF XY: 0.0000537 AC XY: 4AN XY: 74470
ClinVar
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | May 12, 2017 | - - |
Hyperkalemic periodic paralysis Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Oct 04, 2023 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Oct 08, 2020 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at