rs80356468
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2
The NM_001365536.1(SCN9A):c.406A>G(p.Ile136Val) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as not provided (no stars).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
SCN9A
NM_001365536.1 missense
NM_001365536.1 missense
Scores
6
10
2
Clinical Significance
Conservation
PhyloP100: 8.02
Publications
34 publications found
Genes affected
SCN9A (HGNC:10597): (sodium voltage-gated channel alpha subunit 9) This gene encodes a voltage-gated sodium channel which plays a significant role in nociception signaling. Mutations in this gene have been associated with primary erythermalgia, channelopathy-associated insensitivity to pain, and paroxysmal extreme pain disorder. [provided by RefSeq, Aug 2009]
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ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_001365536.1. You can select a different transcript below to see updated ACMG assignments.
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| SCN9A | MANE Select | c.406A>G | p.Ile136Val | missense | Exon 4 of 27 | ENSP00000495601.1 | Q15858-1 | ||
| SCN9A | TSL:5 | c.406A>G | p.Ile136Val | missense | Exon 4 of 27 | ENSP00000304748.7 | Q15858-1 | ||
| SCN9A | TSL:5 | c.406A>G | p.Ile136Val | missense | Exon 4 of 27 | ENSP00000386306.1 | Q15858-3 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1430330Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 708374
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
1430330
Hom.:
Cov.:
31
AF XY:
AC XY:
0
AN XY:
708374
African (AFR)
AF:
AC:
0
AN:
33054
American (AMR)
AF:
AC:
0
AN:
40344
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
25580
East Asian (EAS)
AF:
AC:
0
AN:
38942
South Asian (SAS)
AF:
AC:
0
AN:
81900
European-Finnish (FIN)
AF:
AC:
0
AN:
51704
Middle Eastern (MID)
AF:
AC:
0
AN:
5728
European-Non Finnish (NFE)
AF:
AC:
0
AN:
1093830
Other (OTH)
AF:
AC:
0
AN:
59248
GnomAD4 genome
GnomAD4 genome
Cov.:
32
Alfa
AF:
Hom.:
ClinVar
ClinVar submissions
View on ClinVar Significance:not provided
Revision:no classification provided
Pathogenic
VUS
Benign
Condition
-
-
-
Primary erythromelalgia (1)
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Pathogenic
DANN
Uncertain
DEOGEN2
Uncertain
D
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
D
M_CAP
Uncertain
D
MetaRNN
Uncertain
D
MetaSVM
Pathogenic
D
MutationAssessor
Uncertain
M
PhyloP100
PrimateAI
Uncertain
T
PROVEAN
Benign
N
REVEL
Pathogenic
Sift
Pathogenic
D
Sift4G
Benign
T
Polyphen
B
Vest4
MVP
MPC
ClinPred
D
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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