rs574777861
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_001349253.2(SCN11A):c.760G>T(p.Val254Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000769 in 1,614,050 control chromosomes in the GnomAD database, including 18 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V254I) has been classified as Uncertain significance.
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.760G>T | p.Val254Phe | missense_variant | 10/30 | ENST00000302328.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SCN11A | ENST00000302328.9 | c.760G>T | p.Val254Phe | missense_variant | 10/30 | 5 | NM_001349253.2 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.000434 AC: 66AN: 152180Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.00163 AC: 408AN: 250888Hom.: 4 AF XY: 0.00234 AC XY: 317AN XY: 135570
GnomAD4 exome AF: 0.000803 AC: 1174AN: 1461752Hom.: 17 Cov.: 31 AF XY: 0.00120 AC XY: 872AN XY: 727178
GnomAD4 genome ? AF: 0.000440 AC: 67AN: 152298Hom.: 1 Cov.: 32 AF XY: 0.000698 AC XY: 52AN XY: 74474
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