rs28919895
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_005410.4(SELENOP):c.334C>T(p.Pro112Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000113 in 1,611,540 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/18 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_005410.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SELENOP | NM_005410.4 | c.334C>T | p.Pro112Ser | missense_variant | 3/5 | ENST00000514985.6 | |
SELENOP | NM_001093726.3 | c.424C>T | p.Pro142Ser | missense_variant | 4/6 | ||
SELENOP | NM_001085486.3 | c.334C>T | p.Pro112Ser | missense_variant | 4/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SELENOP | ENST00000514985.6 | c.334C>T | p.Pro112Ser | missense_variant | 3/5 | 1 | NM_005410.4 | P1 | |
ENST00000606056.1 | n.585G>A | non_coding_transcript_exon_variant | 1/1 |
Frequencies
GnomAD3 genomes ? AF: 0.000125 AC: 19AN: 152144Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000293 AC: 73AN: 249192Hom.: 0 AF XY: 0.000229 AC XY: 31AN XY: 135242
GnomAD4 exome AF: 0.000112 AC: 163AN: 1459278Hom.: 0 Cov.: 29 AF XY: 0.000101 AC XY: 73AN XY: 726058
GnomAD4 genome ? AF: 0.000125 AC: 19AN: 152262Hom.: 0 Cov.: 32 AF XY: 0.000188 AC XY: 14AN XY: 74440
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at