rs374257387
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The NM_000334.4(SCN4A):c.1243-5C>A variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000219 in 1,599,096 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_000334.4 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SCN4A | NM_000334.4 | c.1243-5C>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000435607.3 | NP_000325.4 | |||
LOC105371858 | XR_001752969.2 | n.345+32G>T | intron_variant, non_coding_transcript_variant | |||||
LOC105371858 | XR_001752970.2 | n.400+32G>T | intron_variant, non_coding_transcript_variant | |||||
LOC105371858 | XR_934910.3 | n.220+32G>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SCN4A | ENST00000435607.3 | c.1243-5C>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_000334.4 | ENSP00000396320 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152230Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000445 AC: 1AN: 224844Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 121658
GnomAD4 exome AF: 0.0000221 AC: 32AN: 1446866Hom.: 0 Cov.: 32 AF XY: 0.0000153 AC XY: 11AN XY: 718464
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152230Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74362
ClinVar
Submissions by phenotype
Familial hyperkalemic periodic paralysis Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | May 18, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at