chr11-118145097-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_174934.4(SCN4B):āc.194A>Gā(p.His65Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000248 in 1,613,998 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. 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. H65L) has been classified as Likely benign.
Frequency
Consequence
NM_174934.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SCN4B | NM_174934.4 | c.194A>G | p.His65Arg | missense_variant | 2/5 | ENST00000324727.9 | |
SCN4B | NM_001142349.2 | c.-137A>G | 5_prime_UTR_variant | 1/4 | |||
SCN4B | NM_001142348.2 | c.62-3761A>G | intron_variant | ||||
SCN4B | NR_024527.2 | n.337A>G | non_coding_transcript_exon_variant | 1/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SCN4B | ENST00000324727.9 | c.194A>G | p.His65Arg | missense_variant | 2/5 | 1 | NM_174934.4 | P1 | |
SCN4B | ENST00000415030.6 | n.337A>G | non_coding_transcript_exon_variant | 1/4 | 1 | ||||
SCN4B | ENST00000529878.1 | c.62-3761A>G | intron_variant | 4 | |||||
SCN4B | ENST00000532138.1 | n.604A>G | non_coding_transcript_exon_variant | 1/3 | 4 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152118Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461880Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 727244
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152118Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74324
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at