1-25805203-G-A
Variant summary
Our verdict is Likely benign. The variant received -6 ACMG points: 0P and 6B. BP4_StrongBP6BP7
The NM_020451.3(SELENON):c.465G>A(p.Thr155Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000489 in 1,614,014 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_020451.3 synonymous
Scores
Clinical Significance
Conservation
Publications
- rigid spine muscular dystrophy 1Inheritance: AR Classification: DEFINITIVE Submitted by: Ambry Genetics, G2P
- SELENON-related myopathyInheritance: AR Classification: DEFINITIVE Submitted by: ClinGen
- congenital myopathy 4A, autosomal dominantInheritance: AR Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)
- congenital fiber-type disproportion myopathyInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
- desmin-related myopathy with Mallory body-like inclusionsInheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
- rigid spine syndromeInheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
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ACMG classification
Our verdict: Likely_benign. The variant received -6 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SELENON | ENST00000361547.7 | c.465G>A | p.Thr155Thr | synonymous_variant | Exon 4 of 13 | 1 | NM_020451.3 | ENSP00000355141.2 | ||
SELENON | ENST00000374315.1 | c.363G>A | p.Thr121Thr | synonymous_variant | Exon 3 of 12 | 5 | ENSP00000363434.1 | |||
SELENON | ENST00000354177.9 | c.363G>A | p.Thr121Thr | synonymous_variant | Exon 3 of 12 | 5 | ENSP00000346109.5 | |||
SELENON | ENST00000494537.2 | n.363G>A | non_coding_transcript_exon_variant | Exon 3 of 13 | 3 | ENSP00000508308.1 |
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 152192Hom.: 0 Cov.: 31 show subpopulations
GnomAD2 exomes AF: 0.0000441 AC: 11AN: 249450 AF XY: 0.0000369 show subpopulations
GnomAD4 exome AF: 0.0000486 AC: 71AN: 1461822Hom.: 1 Cov.: 34 AF XY: 0.0000591 AC XY: 43AN XY: 727202 show subpopulations
Age Distribution
GnomAD4 genome AF: 0.0000526 AC: 8AN: 152192Hom.: 0 Cov.: 31 AF XY: 0.0000404 AC XY: 3AN XY: 74348 show subpopulations
Age Distribution
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:1
- -
SELENON: BP4, BP7 -
not specified Benign:1
- -
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