2-166406295-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_002976.4(SCN7A):c.4334A>G(p.Asn1445Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000577 in 1,612,992 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_002976.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SCN7A | NM_002976.4 | c.4334A>G | p.Asn1445Ser | missense_variant | 26/26 | ENST00000643258.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SCN7A | ENST00000643258.1 | c.4334A>G | p.Asn1445Ser | missense_variant | 26/26 | NM_002976.4 | P1 | ||
SCN7A | ENST00000441411.2 | c.4334A>G | p.Asn1445Ser | missense_variant | 25/25 | 1 | P1 | ||
SCN7A | ENST00000424326.5 | c.*2139A>G | 3_prime_UTR_variant, NMD_transcript_variant | 26/26 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000527 AC: 8AN: 151888Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000113 AC: 28AN: 248456Hom.: 0 AF XY: 0.000185 AC XY: 25AN XY: 134784
GnomAD4 exome AF: 0.0000582 AC: 85AN: 1461104Hom.: 0 Cov.: 33 AF XY: 0.0000867 AC XY: 63AN XY: 726856
GnomAD4 genome ? AF: 0.0000527 AC: 8AN: 151888Hom.: 0 Cov.: 32 AF XY: 0.0000809 AC XY: 6AN XY: 74168
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 10, 2023 | The c.4334A>G (p.N1445S) alteration is located in exon 25 (coding exon 24) of the SCN7A gene. This alteration results from a A to G substitution at nucleotide position 4334, causing the asparagine (N) at amino acid position 1445 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at