chr19-35030781-C-G
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_ModerateBP6_ModerateBS1BS2
The NM_001037.5(SCN1B):c.-40C>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000703 in 867,226 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 Benign (★).
Frequency
Consequence
NM_001037.5 5_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SCN1B | ENST00000262631 | c.-40C>G | 5_prime_UTR_variant | Exon 1 of 6 | 1 | NM_001037.5 | ENSP00000262631.3 | |||
SCN1B | ENST00000415950 | c.-40C>G | 5_prime_UTR_variant | Exon 1 of 3 | 1 | ENSP00000396915.2 | ||||
SCN1B | ENST00000638536 | c.-40C>G | 5_prime_UTR_variant | Exon 1 of 5 | 1 | ENSP00000492022.1 | ||||
SCN1B | ENST00000595652 | c.-40C>G | 5_prime_UTR_variant | Exon 1 of 6 | 2 | ENSP00000468848.1 |
Frequencies
GnomAD3 genomes AF: 0.0000536 AC: 8AN: 149306Hom.: 0 Cov.: 31
GnomAD4 exome AF: 0.0000738 AC: 53AN: 717920Hom.: 0 Cov.: 10 AF XY: 0.0000932 AC XY: 34AN XY: 364694
GnomAD4 genome AF: 0.0000536 AC: 8AN: 149306Hom.: 0 Cov.: 31 AF XY: 0.0000550 AC XY: 4AN XY: 72770
ClinVar
Submissions by phenotype
not specified Benign:1
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at