rs3877899
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_005410.4(SELENOP):c.700G>T(p.Ala234Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,892 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/18 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 variant affecting the same amino acid position, but resulting in a different missense (i.e. A234T) has been classified as Likely benign.
Frequency
Consequence
NM_005410.4 missense
Scores
Clinical Significance
Conservation
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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.700G>T | p.Ala234Ser | missense_variant | 5/5 | ENST00000514985.6 | |
CCDC152 | NM_001134848.2 | c.*1385C>A | 3_prime_UTR_variant | 9/9 | ENST00000361970.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SELENOP | ENST00000514985.6 | c.700G>T | p.Ala234Ser | missense_variant | 5/5 | 1 | NM_005410.4 | P1 | |
CCDC152 | ENST00000361970.10 | c.*1385C>A | 3_prime_UTR_variant | 9/9 | 1 | NM_001134848.2 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.00000405 AC: 1AN: 247196Hom.: 0 AF XY: 0.00000744 AC XY: 1AN XY: 134328
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461892Hom.: 0 Cov.: 36 AF XY: 0.00000138 AC XY: 1AN XY: 727246
GnomAD4 genome ? Cov.: 32
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at