rs199791077
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_001365536.1(SCN9A):āc.3561G>Cā(p.Lys1187Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000221 in 1,582,598 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ).
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.3561G>C | p.Lys1187Asn | missense_variant | 19/27 | ENST00000642356.2 | |
SCN1A-AS1 | NR_110260.1 | n.612-5627C>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SCN9A | ENST00000642356.2 | c.3561G>C | p.Lys1187Asn | missense_variant | 19/27 | NM_001365536.1 | P1 | ||
SCN1A-AS1 | ENST00000651574.1 | n.1290-5627C>G | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.0000921 AC: 14AN: 152090Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000603 AC: 12AN: 199082Hom.: 0 AF XY: 0.0000566 AC XY: 6AN XY: 105952
GnomAD4 exome AF: 0.0000133 AC: 19AN: 1430390Hom.: 0 Cov.: 30 AF XY: 0.0000141 AC XY: 10AN XY: 708274
GnomAD4 genome ? AF: 0.000105 AC: 16AN: 152208Hom.: 0 Cov.: 32 AF XY: 0.0000941 AC XY: 7AN XY: 74406
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 | Dec 11, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at