rs562551941
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6_Very_StrongBP7
The NM_000334.4(SCN4A):c.4719C>T(p.Ile1573=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000397 in 1,614,038 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. I1573I) 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 -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SCN4A | NM_000334.4 | c.4719C>T | p.Ile1573= | synonymous_variant | 24/24 | ENST00000435607.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SCN4A | ENST00000435607.3 | c.4719C>T | p.Ile1573= | synonymous_variant | 24/24 | 1 | NM_000334.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000658 AC: 10AN: 152060Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000560 AC: 14AN: 249870Hom.: 0 AF XY: 0.0000369 AC XY: 5AN XY: 135552
GnomAD4 exome AF: 0.0000369 AC: 54AN: 1461860Hom.: 0 Cov.: 35 AF XY: 0.0000330 AC XY: 24AN XY: 727226
GnomAD4 genome ? AF: 0.0000657 AC: 10AN: 152178Hom.: 0 Cov.: 31 AF XY: 0.0000538 AC XY: 4AN XY: 74404
ClinVar
Submissions by phenotype
Hyperkalemic periodic paralysis Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 21, 2023 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jun 01, 2022 | SCN4A: BP4, BP7 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at