1-25808592-G-C
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_020451.3(SELENON):c.550G>C(p.Ala184Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00049 in 1,613,288 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A184T) has been classified as Uncertain significance.
Frequency
Consequence
NM_020451.3 missense
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 |
---|---|---|---|---|---|---|---|---|---|---|
SELENON | ENST00000361547.7 | c.550G>C | p.Ala184Pro | missense_variant | Exon 5 of 13 | 1 | NM_020451.3 | ENSP00000355141.2 | ||
SELENON | ENST00000374315.1 | c.448G>C | p.Ala150Pro | missense_variant | Exon 4 of 12 | 5 | ENSP00000363434.1 | |||
SELENON | ENST00000354177.9 | c.448G>C | p.Ala150Pro | missense_variant | Exon 4 of 12 | 5 | ENSP00000346109.5 | |||
SELENON | ENST00000494537.2 | n.448G>C | non_coding_transcript_exon_variant | Exon 4 of 13 | 3 | ENSP00000508308.1 |
Frequencies
GnomAD3 genomes AF: 0.00261 AC: 396AN: 151708Hom.: 2 Cov.: 33
GnomAD3 exomes AF: 0.000694 AC: 172AN: 247778Hom.: 0 AF XY: 0.000468 AC XY: 63AN XY: 134628
GnomAD4 exome AF: 0.000267 AC: 390AN: 1461460Hom.: 0 Cov.: 32 AF XY: 0.000215 AC XY: 156AN XY: 727036
GnomAD4 genome AF: 0.00264 AC: 401AN: 151828Hom.: 2 Cov.: 33 AF XY: 0.00249 AC XY: 185AN XY: 74204
ClinVar
Submissions by phenotype
Eichsfeld type congenital muscular dystrophy Uncertain:1Benign:1
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not provided Benign:2
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SELENON-related disorder Benign:1
This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
SEPN1-related disorder Benign:1
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at