rs200211620
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_001349253.2(SCN11A):c.2201A>G(p.Lys734Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000774 in 1,614,072 control chromosomes in the GnomAD database, including 17 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 -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SCN11A | NM_001349253.2 | c.2201A>G | p.Lys734Arg | missense_variant | 18/30 | ENST00000302328.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SCN11A | ENST00000302328.9 | c.2201A>G | p.Lys734Arg | missense_variant | 18/30 | 5 | NM_001349253.2 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.000441 AC: 67AN: 152080Hom.: 1 Cov.: 31
GnomAD3 exomes AF: 0.00164 AC: 411AN: 251196Hom.: 4 AF XY: 0.00234 AC XY: 317AN XY: 135752
GnomAD4 exome AF: 0.000809 AC: 1183AN: 1461874Hom.: 16 Cov.: 34 AF XY: 0.00121 AC XY: 879AN XY: 727238
GnomAD4 genome ? AF: 0.000440 AC: 67AN: 152198Hom.: 1 Cov.: 31 AF XY: 0.000685 AC XY: 51AN XY: 74414
ClinVar
Submissions by phenotype
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 | Invitae | Jan 04, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at