11-118141280-T-A
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM1PM2
The NM_174934.4(SCN4B):c.520A>T(p.Ile174Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000186 in 1,612,622 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. I174V) has been classified as Likely benign.
Frequency
Consequence
NM_174934.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SCN4B | NM_174934.4 | c.520A>T | p.Ile174Phe | missense_variant | 4/5 | ENST00000324727.9 | |
SCN4B | NM_001142349.2 | c.190A>T | p.Ile64Phe | missense_variant | 3/4 | ||
SCN4B | NM_001142348.2 | c.118A>T | p.Ile40Phe | missense_variant | 2/3 | ||
SCN4B | NR_024527.2 | n.509A>T | non_coding_transcript_exon_variant | 3/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SCN4B | ENST00000324727.9 | c.520A>T | p.Ile174Phe | missense_variant | 4/5 | 1 | NM_174934.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152136Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251458Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135902
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1460486Hom.: 0 Cov.: 33 AF XY: 0.00000275 AC XY: 2AN XY: 726560
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152136Hom.: 0 Cov.: 31 AF XY: 0.0000135 AC XY: 1AN XY: 74310
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at