chr2-166272826-T-C
Variant summary
Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_ModerateBP6_Moderate
The NM_001365536.1(SCN9A):c.2924A>G(p.Asn975Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000152 in 1,517,338 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. N975Y) has been classified as Uncertain significance.
Frequency
Consequence
NM_001365536.1 missense
Scores
Clinical Significance
Conservation
Publications
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ACMG classification
Our verdict: Likely_benign. The variant received -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SCN9A | NM_001365536.1 | c.2924A>G | p.Asn975Ser | missense_variant | Exon 17 of 27 | ENST00000642356.2 | NP_001352465.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SCN9A | ENST00000642356.2 | c.2924A>G | p.Asn975Ser | missense_variant | Exon 17 of 27 | NM_001365536.1 | ENSP00000495601.1 | |||
SCN9A | ENST00000303354.11 | c.2924A>G | p.Asn975Ser | missense_variant | Exon 17 of 27 | 5 | ENSP00000304748.7 | |||
SCN9A | ENST00000409672.5 | c.2891A>G | p.Asn964Ser | missense_variant | Exon 17 of 27 | 5 | ENSP00000386306.1 | |||
SCN9A | ENST00000645907.1 | c.2891A>G | p.Asn964Ser | missense_variant | Exon 17 of 27 | ENSP00000495983.1 |
Frequencies
GnomAD3 genomes AF: 0.0000791 AC: 12AN: 151790Hom.: 0 Cov.: 31 show subpopulations
GnomAD2 exomes AF: 0.0000174 AC: 3AN: 172900 AF XY: 0.0000110 show subpopulations
GnomAD4 exome AF: 0.00000806 AC: 11AN: 1365430Hom.: 0 Cov.: 31 AF XY: 0.0000120 AC XY: 8AN XY: 669206 show subpopulations
Age Distribution
GnomAD4 genome AF: 0.0000790 AC: 12AN: 151908Hom.: 0 Cov.: 31 AF XY: 0.0000539 AC XY: 4AN XY: 74204 show subpopulations
Age Distribution
ClinVar
Submissions by phenotype
Generalized epilepsy with febrile seizures plus, type 7;C2752089:Neuropathy, hereditary sensory and autonomic, type 2A Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at