chr2-165146815-A-G
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 1P and 12B. PP2BP4_ModerateBP6_ModerateBS1BS2
The NM_006922.4(SCN3A):āc.1595T>Cā(p.Val532Ala) variant causes a missense change. The variant allele was found at a frequency of 0.00000867 in 1,614,032 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 (ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V532D) has been classified as Uncertain significance.
Frequency
Consequence
NM_006922.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SCN3A | NM_006922.4 | c.1595T>C | p.Val532Ala | missense_variant | 12/28 | ENST00000283254.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SCN3A | ENST00000283254.12 | c.1595T>C | p.Val532Ala | missense_variant | 12/28 | 1 | NM_006922.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000723 AC: 11AN: 152120Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000159 AC: 4AN: 251376Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135852
GnomAD4 exome AF: 0.00000205 AC: 3AN: 1461794Hom.: 0 Cov.: 30 AF XY: 0.00000275 AC XY: 2AN XY: 727196
GnomAD4 genome AF: 0.0000723 AC: 11AN: 152238Hom.: 0 Cov.: 31 AF XY: 0.000108 AC XY: 8AN XY: 74414
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 22, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at