11-118166891-T-A
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 1P and 4B. PP3BS2
The NM_004588.5(SCN2B):c.644A>T(p.Lys215Met) variant causes a missense change. The variant allele was found at a frequency of 0.00000929 in 1,613,844 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic 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 -3 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SCN2B | ENST00000278947.6 | c.644A>T | p.Lys215Met | missense_variant | Exon 4 of 4 | 1 | NM_004588.5 | ENSP00000278947.5 | ||
SCN2B | ENST00000658882.1 | n.*469A>T | non_coding_transcript_exon_variant | Exon 5 of 5 | ENSP00000499572.1 | |||||
SCN2B | ENST00000669850.1 | n.886A>T | non_coding_transcript_exon_variant | Exon 4 of 4 | ||||||
SCN2B | ENST00000658882.1 | n.*469A>T | 3_prime_UTR_variant | Exon 5 of 5 | ENSP00000499572.1 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152128Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000119 AC: 3AN: 251380Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135860
GnomAD4 exome AF: 0.00000889 AC: 13AN: 1461716Hom.: 0 Cov.: 31 AF XY: 0.00000963 AC XY: 7AN XY: 727168
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152128Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74310
ClinVar
Submissions by phenotype
Cardiovascular phenotype Uncertain:1
The c.644A>T (p.K215M) alteration is located in exon 4 (coding exon 4) of the SCN2B gene. This alteration results from a A to T substitution at nucleotide position 644, causing the lysine (K) at amino acid position 215 to be replaced by a methionine (M). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at