rs1275085
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BA1
The NM_001040151.2(SCN3B):c.438C>T(p.Thr146=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0859 in 1,613,836 control chromosomes in the GnomAD database, including 6,568 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Synonymous variant affecting the same amino acid position (i.e. T146T) has been classified as Benign.
Frequency
Consequence
NM_001040151.2 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -19 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SCN3B | NM_001040151.2 | c.438C>T | p.Thr146= | synonymous_variant | 4/7 | ENST00000299333.8 | |
SCN3B | NM_018400.4 | c.438C>T | p.Thr146= | synonymous_variant | 3/6 | ||
SCN3B | XM_011542897.3 | c.438C>T | p.Thr146= | synonymous_variant | 4/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SCN3B | ENST00000299333.8 | c.438C>T | p.Thr146= | synonymous_variant | 4/7 | 1 | NM_001040151.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0882 AC: 13401AN: 152002Hom.: 647 Cov.: 32
GnomAD3 exomes AF: 0.0864 AC: 21697AN: 251046Hom.: 1168 AF XY: 0.0920 AC XY: 12483AN XY: 135724
GnomAD4 exome AF: 0.0856 AC: 125191AN: 1461716Hom.: 5920 Cov.: 33 AF XY: 0.0883 AC XY: 64235AN XY: 727182
GnomAD4 genome ? AF: 0.0881 AC: 13401AN: 152120Hom.: 648 Cov.: 32 AF XY: 0.0892 AC XY: 6635AN XY: 74372
ClinVar
Submissions by phenotype
not specified Benign:2
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Benign, criteria provided, single submitter | clinical testing | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Apr 09, 2023 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 03, 2015 | - - |
Cardiovascular phenotype Benign:1
Benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 23, 2015 | This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Brugada syndrome 7 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at