chr19-35033954-C-G
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The ENST00000415950.5(SCN1B):āc.663C>Gā(p.Val221=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000837 in 1,553,224 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 (ā ). Synonymous variant affecting the same amino acid position (i.e. V221V) has been classified as Likely benign.
Frequency
Consequence
ENST00000415950.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SCN1B | NM_001037.5 | c.448+215C>G | intron_variant | ENST00000262631.11 | |||
SCN1B | NM_199037.5 | c.663C>G | p.Val221= | synonymous_variant | 3/3 | ||
SCN1B | NM_001321605.2 | c.349+215C>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SCN1B | ENST00000262631.11 | c.448+215C>G | intron_variant | 1 | NM_001037.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152248Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000637 AC: 1AN: 157042Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 83016
GnomAD4 exome AF: 0.00000857 AC: 12AN: 1400976Hom.: 0 Cov.: 33 AF XY: 0.00000579 AC XY: 4AN XY: 691322
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152248Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74378
ClinVar
Submissions by phenotype
Brugada syndrome 5 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 19, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at