rs187880136
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_ModerateBP6_Very_StrongBP7BS1
The NM_020451.3(SELENON):c.852C>T(p.Phe284Phe) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000226 in 1,613,792 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 (★★).
Frequency
Consequence
NM_020451.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -15 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SELENON | ENST00000361547.7 | c.852C>T | p.Phe284Phe | synonymous_variant | Exon 6 of 13 | 1 | NM_020451.3 | ENSP00000355141.2 | ||
SELENON | ENST00000374315.1 | c.750C>T | p.Phe250Phe | synonymous_variant | Exon 5 of 12 | 5 | ENSP00000363434.1 | |||
SELENON | ENST00000354177.9 | c.681C>T | p.Phe227Phe | synonymous_variant | Exon 5 of 12 | 5 | ENSP00000346109.5 | |||
SELENON | ENST00000494537.2 | n.750C>T | non_coding_transcript_exon_variant | Exon 5 of 13 | 3 | ENSP00000508308.1 |
Frequencies
GnomAD3 genomes AF: 0.00130 AC: 198AN: 152250Hom.: 1 Cov.: 33
GnomAD3 exomes AF: 0.000333 AC: 83AN: 249268Hom.: 0 AF XY: 0.000273 AC XY: 37AN XY: 135370
GnomAD4 exome AF: 0.000114 AC: 166AN: 1461424Hom.: 1 Cov.: 33 AF XY: 0.0000977 AC XY: 71AN XY: 727024
GnomAD4 genome AF: 0.00130 AC: 198AN: 152368Hom.: 1 Cov.: 33 AF XY: 0.00129 AC XY: 96AN XY: 74504
ClinVar
Submissions by phenotype
not provided Benign:3
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SELENON: BP4 -
SELENON-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Eichsfeld type congenital muscular dystrophy Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at