rs74401238
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_001365536.1(SCN9A):āc.3362G>Cā(p.Arg1121Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000279 in 1,612,082 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R1121Q) has been classified as Likely benign.
Frequency
Consequence
NM_001365536.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SCN9A | NM_001365536.1 | c.3362G>C | p.Arg1121Pro | missense_variant | 18/27 | ENST00000642356.2 | |
SCN1A-AS1 | NR_110260.1 | n.832C>G | non_coding_transcript_exon_variant | 7/12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SCN9A | ENST00000642356.2 | c.3362G>C | p.Arg1121Pro | missense_variant | 18/27 | NM_001365536.1 | P1 | ||
SCN1A-AS1 | ENST00000651574.1 | n.1510C>G | non_coding_transcript_exon_variant | 14/19 |
Frequencies
GnomAD3 genomes ? AF: 0.000125 AC: 19AN: 151888Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000847 AC: 21AN: 247896Hom.: 0 AF XY: 0.0000892 AC XY: 12AN XY: 134470
GnomAD4 exome AF: 0.0000178 AC: 26AN: 1460076Hom.: 0 Cov.: 31 AF XY: 0.0000193 AC XY: 14AN XY: 726300
GnomAD4 genome ? AF: 0.000125 AC: 19AN: 152006Hom.: 0 Cov.: 32 AF XY: 0.000148 AC XY: 11AN XY: 74284
ClinVar
Submissions by phenotype
Generalized epilepsy with febrile seizures plus, type 7;C2752089:Neuropathy, hereditary sensory and autonomic, type 2A Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 27, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at