3-38904075-G-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_001349253.2(SCN11A):c.1632C>A(p.Leu544Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000152 in 1,585,972 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 (★★).
Frequency
Consequence
NM_001349253.2 synonymous
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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SCN11A | NM_001349253.2 | c.1632C>A | p.Leu544Leu | synonymous_variant | Exon 16 of 30 | ENST00000302328.9 | NP_001336182.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000125 AC: 19AN: 152156Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000389 AC: 88AN: 226470Hom.: 0 AF XY: 0.000418 AC XY: 51AN XY: 122010
GnomAD4 exome AF: 0.000155 AC: 222AN: 1433698Hom.: 0 Cov.: 31 AF XY: 0.000172 AC XY: 122AN XY: 711322
GnomAD4 genome AF: 0.000125 AC: 19AN: 152274Hom.: 0 Cov.: 32 AF XY: 0.000134 AC XY: 10AN XY: 74444
ClinVar
Submissions by phenotype
Inborn genetic diseases Benign:1
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
not provided Benign:1
SCN11A: BS1, BS2 -
Hereditary sensory and autonomic neuropathy type 7;C3809899:Familial episodic pain syndrome with predominantly lower limb involvement Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at