chr2-166405659-T-C
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BA1
The NM_002976.4(SCN7A):āc.4970A>Gā(p.Asp1657Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0912 in 1,612,570 control chromosomes in the GnomAD database, including 7,450 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 (no stars). 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 -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SCN7A | NM_002976.4 | c.4970A>G | p.Asp1657Gly | missense_variant | 26/26 | ENST00000643258.1 | NP_002967.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SCN7A | ENST00000643258.1 | c.4970A>G | p.Asp1657Gly | missense_variant | 26/26 | NM_002976.4 | ENSP00000496114.1 | |||
SCN7A | ENST00000441411.2 | c.4970A>G | p.Asp1657Gly | missense_variant | 25/25 | 1 | ENSP00000403846.2 | |||
SCN7A | ENST00000424326.5 | n.*2775A>G | non_coding_transcript_exon_variant | 26/26 | 1 | ENSP00000396600.1 | ||||
SCN7A | ENST00000424326.5 | n.*2775A>G | 3_prime_UTR_variant | 26/26 | 1 | ENSP00000396600.1 |
Frequencies
GnomAD3 genomes AF: 0.0757 AC: 11508AN: 152036Hom.: 526 Cov.: 32
GnomAD3 exomes AF: 0.0850 AC: 21085AN: 248152Hom.: 1092 AF XY: 0.0887 AC XY: 11943AN XY: 134620
GnomAD4 exome AF: 0.0929 AC: 135616AN: 1460416Hom.: 6924 Cov.: 33 AF XY: 0.0942 AC XY: 68455AN XY: 726502
GnomAD4 genome AF: 0.0756 AC: 11507AN: 152154Hom.: 526 Cov.: 32 AF XY: 0.0732 AC XY: 5449AN XY: 74390
ClinVar
Submissions by phenotype
SCN7A-related disorder Benign:1
Benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Nov 26, 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