chr2-165139551-T-C
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 1P and 13B. PP2BP4_StrongBP6BS1BS2
The NM_006922.4(SCN3A):āc.2077A>Gā(p.Met693Val) variant causes a missense change. The variant allele was found at a frequency of 0.000172 in 1,613,980 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 Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. M693T) has been classified as Uncertain significance.
Frequency
Consequence
NM_006922.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SCN3A | NM_006922.4 | c.2077A>G | p.Met693Val | missense_variant | 14/28 | ENST00000283254.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SCN3A | ENST00000283254.12 | c.2077A>G | p.Met693Val | missense_variant | 14/28 | 1 | NM_006922.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000191 AC: 29AN: 152176Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000342 AC: 86AN: 251180Hom.: 0 AF XY: 0.000442 AC XY: 60AN XY: 135748
GnomAD4 exome AF: 0.000170 AC: 248AN: 1461686Hom.: 0 Cov.: 30 AF XY: 0.000235 AC XY: 171AN XY: 727142
GnomAD4 genome AF: 0.000190 AC: 29AN: 152294Hom.: 0 Cov.: 32 AF XY: 0.000255 AC XY: 19AN XY: 74464
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:1
Uncertain significance, criteria provided, single submitter | clinical testing | Mayo Clinic Laboratories, Mayo Clinic | May 02, 2016 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 02, 2024 | - - |
SCN3A-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Feb 04, 2022 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at