3-38883320-G-C
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_001349253.2(SCN11A):c.3132C>G(p.Asn1044Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00102 in 1,613,948 control chromosomes in the GnomAD database, including 8 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SCN11A | NM_001349253.2 | c.3132C>G | p.Asn1044Lys | missense_variant | Exon 22 of 30 | ENST00000302328.9 | NP_001336182.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00353 AC: 537AN: 152130Hom.: 3 Cov.: 32
GnomAD3 exomes AF: 0.00113 AC: 283AN: 251240Hom.: 2 AF XY: 0.000759 AC XY: 103AN XY: 135772
GnomAD4 exome AF: 0.000754 AC: 1102AN: 1461700Hom.: 5 Cov.: 31 AF XY: 0.000700 AC XY: 509AN XY: 727162
GnomAD4 genome AF: 0.00361 AC: 550AN: 152248Hom.: 3 Cov.: 32 AF XY: 0.00347 AC XY: 258AN XY: 74436
ClinVar
Submissions by phenotype
not provided Benign:4
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This variant is associated with the following publications: (PMID: 29264398) -
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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. -
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