rs779905648
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_ModerateBP7BS2
The NM_006514.4(SCN10A):c.4137C>T(p.Ser1379=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000821 in 1,461,288 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. S1379S) has been classified as Likely benign.
Frequency
Consequence
NM_006514.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SCN10A | NM_006514.4 | c.4137C>T | p.Ser1379= | synonymous_variant | 24/28 | ENST00000449082.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SCN10A | ENST00000449082.3 | c.4137C>T | p.Ser1379= | synonymous_variant | 24/28 | 1 | NM_006514.4 | P4 | |
SCN10A | ENST00000655275.1 | c.4161C>T | p.Ser1387= | synonymous_variant | 24/28 | ||||
SCN10A | ENST00000643924.1 | c.4134C>T | p.Ser1378= | synonymous_variant | 23/27 | A1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000399 AC: 1AN: 250448Hom.: 0 AF XY: 0.00000739 AC XY: 1AN XY: 135342
GnomAD4 exome AF: 0.00000821 AC: 12AN: 1461288Hom.: 0 Cov.: 30 AF XY: 0.00000688 AC XY: 5AN XY: 726904
GnomAD4 genome Cov.: 32
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at