chr2-166423412-C-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_002976.4(SCN7A):c.2874G>T(p.Met958Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.699 in 1,574,744 control chromosomes in the GnomAD database, including 387,363 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_002976.4 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 |
---|---|---|---|---|---|---|---|
SCN7A | NM_002976.4 | c.2874G>T | p.Met958Ile | missense_variant | 19/26 | ENST00000643258.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SCN7A | ENST00000643258.1 | c.2874G>T | p.Met958Ile | missense_variant | 19/26 | NM_002976.4 | P1 | ||
SCN7A | ENST00000441411.2 | c.2874G>T | p.Met958Ile | missense_variant | 18/25 | 1 | P1 | ||
SCN7A | ENST00000424326.5 | c.*679G>T | 3_prime_UTR_variant, NMD_transcript_variant | 19/26 | 1 |
Frequencies
GnomAD3 genomes AF: 0.748 AC: 113479AN: 151630Hom.: 43476 Cov.: 30
GnomAD3 exomes AF: 0.696 AC: 144203AN: 207238Hom.: 50161 AF XY: 0.691 AC XY: 77579AN XY: 112280
GnomAD4 exome AF: 0.694 AC: 987357AN: 1422994Hom.: 343827 Cov.: 32 AF XY: 0.693 AC XY: 489923AN XY: 706642
GnomAD4 genome AF: 0.749 AC: 113597AN: 151750Hom.: 43536 Cov.: 30 AF XY: 0.746 AC XY: 55276AN XY: 74140
ClinVar
Submissions by phenotype
SCN7A-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 17, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at