rs543502873
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_000334.4(SCN4A):āc.448A>Cā(p.Met150Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000112 in 1,613,588 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ).
Frequency
Consequence
NM_000334.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SCN4A | NM_000334.4 | c.448A>C | p.Met150Leu | missense_variant | 3/24 | ENST00000435607.3 | NP_000325.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SCN4A | ENST00000435607.3 | c.448A>C | p.Met150Leu | missense_variant | 3/24 | 1 | NM_000334.4 | ENSP00000396320 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000855 AC: 13AN: 152124Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000245 AC: 61AN: 248580Hom.: 1 AF XY: 0.000378 AC XY: 51AN XY: 134858
GnomAD4 exome AF: 0.000115 AC: 168AN: 1461346Hom.: 2 Cov.: 31 AF XY: 0.000176 AC XY: 128AN XY: 726934
GnomAD4 genome AF: 0.0000854 AC: 13AN: 152242Hom.: 0 Cov.: 32 AF XY: 0.000107 AC XY: 8AN XY: 74440
ClinVar
Submissions by phenotype
Familial hyperkalemic periodic paralysis Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Sep 26, 2022 | - - |
Paramyotonia congenita of Von Eulenburg;C0238357:Familial hyperkalemic periodic paralysis;C2750061:Hypokalemic periodic paralysis, type 2;C2931826:Potassium-aggravated myotonia;C3280112:Congenital myasthenic syndrome 16;C3714580:Hypokalemic periodic paralysis, type 1 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Sep 07, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at