rs370917734
Positions:
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The ENST00000449082.3(SCN10A):c.390-9G>C variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000209 in 1,436,618 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0000021 ( 0 hom. )
Consequence
SCN10A
ENST00000449082.3 splice_polypyrimidine_tract, intron
ENST00000449082.3 splice_polypyrimidine_tract, intron
Scores
2
Splicing: ADA: 0.00008747
1
Clinical Significance
Conservation
PhyloP100: -0.900
Genes affected
SCN10A (HGNC:10582): (sodium voltage-gated channel alpha subunit 10) The protein encoded by this gene is a tetrodotoxin-resistant voltage-gated sodium channel alpha subunit. The properties of the channel formed by the encoded transmembrane protein can be altered by interaction with different beta subunits. This protein may be involved in the onset of pain associated with peripheral neuropathy. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jun 2014]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.72).
BP6
Variant 3-38789045-C-G is Benign according to our data. Variant chr3-38789045-C-G is described in ClinVar as [Likely_benign]. Clinvar id is 1608896.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SCN10A | NM_006514.4 | c.390-9G>C | splice_polypyrimidine_tract_variant, intron_variant | ENST00000449082.3 | NP_006505.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SCN10A | ENST00000449082.3 | c.390-9G>C | splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_006514.4 | ENSP00000390600 | P4 | |||
SCN10A | ENST00000643924.1 | c.390-9G>C | splice_polypyrimidine_tract_variant, intron_variant | ENSP00000495595 | A1 | |||||
SCN10A | ENST00000655275.1 | c.390-9G>C | splice_polypyrimidine_tract_variant, intron_variant | ENSP00000499510 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
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32
GnomAD3 exomes AF: 0.00000800 AC: 2AN: 250148Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135222
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GnomAD4 exome AF: 0.00000209 AC: 3AN: 1436618Hom.: 0 Cov.: 26 AF XY: 0.00000419 AC XY: 3AN XY: 716356
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GnomAD4 genome Cov.: 32
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Brugada syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Nov 15, 2022 | - - |
Computational scores
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Name
Calibrated prediction
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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dbscSNV1_ADA
Benign
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at