3-38894643-C-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001349253.2(SCN11A):c.2725G>A(p.Val909Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.233 in 1,613,770 control chromosomes in the GnomAD database, including 45,755 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_001349253.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SCN11A | NM_001349253.2 | c.2725G>A | p.Val909Ile | missense_variant | 19/30 | ENST00000302328.9 | NP_001336182.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SCN11A | ENST00000302328.9 | c.2725G>A | p.Val909Ile | missense_variant | 19/30 | 5 | NM_001349253.2 | ENSP00000307599.3 |
Frequencies
GnomAD3 genomes AF: 0.202 AC: 30746AN: 152026Hom.: 3480 Cov.: 32
GnomAD3 exomes AF: 0.221 AC: 55576AN: 251334Hom.: 6539 AF XY: 0.221 AC XY: 29960AN XY: 135820
GnomAD4 exome AF: 0.236 AC: 345595AN: 1461626Hom.: 42277 Cov.: 34 AF XY: 0.235 AC XY: 170820AN XY: 727108
GnomAD4 genome AF: 0.202 AC: 30753AN: 152144Hom.: 3478 Cov.: 32 AF XY: 0.202 AC XY: 15048AN XY: 74372
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Aug 06, 2018 | This variant is associated with the following publications: (PMID: 27224030, 28953656) - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Familial episodic pain syndrome with predominantly lower limb involvement Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 15, 2021 | - - |
Hereditary sensory and autonomic neuropathy type 7 Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 15, 2021 | - - |
Hereditary sensory and autonomic neuropathy type 7;C3809899:Familial episodic pain syndrome with predominantly lower limb involvement Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Feb 01, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at