rs2304016
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001040142.2(SCN2A):c.971-32A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00512 in 1,537,156 control chromosomes in the GnomAD database, including 189 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). There are indicators that this mutation may affect the branch point..
Frequency
Consequence
NM_001040142.2 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SCN2A | ENST00000375437.7 | c.971-32A>G | intron_variant | Intron 7 of 26 | 5 | NM_001040142.2 | ENSP00000364586.2 | |||
SCN2A | ENST00000631182.3 | c.971-32A>G | intron_variant | Intron 7 of 26 | 5 | NM_001371246.1 | ENSP00000486885.1 | |||
SCN2A | ENST00000283256.10 | c.971-32A>G | intron_variant | Intron 7 of 26 | 1 | ENSP00000283256.6 | ||||
SCN2A | ENST00000424833.5 | c.971-32A>G | intron_variant | Intron 7 of 10 | 1 | ENSP00000406454.2 |
Frequencies
GnomAD3 genomes AF: 0.00584 AC: 888AN: 152130Hom.: 20 Cov.: 32
GnomAD3 exomes AF: 0.0119 AC: 2907AN: 244650Hom.: 77 AF XY: 0.0108 AC XY: 1423AN XY: 132278
GnomAD4 exome AF: 0.00505 AC: 6990AN: 1384906Hom.: 169 Cov.: 21 AF XY: 0.00505 AC XY: 3501AN XY: 693192
GnomAD4 genome AF: 0.00581 AC: 884AN: 152250Hom.: 20 Cov.: 32 AF XY: 0.00705 AC XY: 525AN XY: 74446
ClinVar
Submissions by phenotype
not provided Benign:2
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at