11-118166901-C-G
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_004588.5(SCN2B):c.634G>C(p.Asp212His) variant causes a missense change. The variant allele was found at a frequency of 0.00000479 in 1,461,788 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 Uncertain significance (★).
Frequency
Consequence
NM_004588.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SCN2B | ENST00000278947.6 | c.634G>C | p.Asp212His | missense_variant | Exon 4 of 4 | 1 | NM_004588.5 | ENSP00000278947.5 | ||
SCN2B | ENST00000658882.1 | n.*459G>C | non_coding_transcript_exon_variant | Exon 5 of 5 | ENSP00000499572.1 | |||||
SCN2B | ENST00000669850.1 | n.876G>C | non_coding_transcript_exon_variant | Exon 4 of 4 | ||||||
SCN2B | ENST00000658882.1 | n.*459G>C | 3_prime_UTR_variant | Exon 5 of 5 | ENSP00000499572.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251428Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135888
GnomAD4 exome AF: 0.00000479 AC: 7AN: 1461788Hom.: 0 Cov.: 31 AF XY: 0.00000550 AC XY: 4AN XY: 727194
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Cardiovascular phenotype Uncertain:1
The p.D212H variant (also known as c.634G>C), located in coding exon 4 of the SCN2B gene, results from a G to C substitution at nucleotide position 634. The aspartic acid at codon 212 is replaced by histidine, an amino acid with similar properties. This amino acid position is conserved. In addition, the in silico prediction for this alteration is inconclusive. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at