1-25800239-G-C
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 2P and 13B. PM2BP4_StrongBP6_Very_StrongBP7
The NM_020451.3(SELENON):c.9G>C(p.Arg3=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000275 in 145,484 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 (★★). Synonymous variant affecting the same amino acid position (i.e. R3R) has been classified as Likely benign.
Frequency
Consequence
NM_020451.3 synonymous
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 |
---|---|---|---|---|---|---|---|
SELENON | NM_020451.3 | c.9G>C | p.Arg3= | synonymous_variant | 1/13 | ENST00000361547.7 | |
SELENON | NM_206926.2 | c.9G>C | p.Arg3= | synonymous_variant | 1/12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SELENON | ENST00000361547.7 | c.9G>C | p.Arg3= | synonymous_variant | 1/13 | 1 | NM_020451.3 | ||
SELENON | ENST00000374315.1 | c.9G>C | p.Arg3= | synonymous_variant | 1/12 | 5 | P1 | ||
SELENON | ENST00000354177.9 | c.9G>C | p.Arg3= | synonymous_variant | 1/12 | 5 | |||
SELENON | ENST00000494537.2 | c.9G>C | p.Arg3= | synonymous_variant, NMD_transcript_variant | 1/13 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000275 AC: 4AN: 145484Hom.: 0 Cov.: 30
GnomAD4 exome Cov.: 9
GnomAD4 genome ? AF: 0.0000275 AC: 4AN: 145484Hom.: 0 Cov.: 30 AF XY: 0.0000283 AC XY: 2AN XY: 70724
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 04, 2016 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
Eichsfeld type congenital muscular dystrophy Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Aug 10, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at