rs776875257
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001172437.2(PEG10):c.439C>A(p.Pro147Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,460,404 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/19 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. P147S) has been classified as Uncertain significance.
Frequency
Consequence
NM_001172437.2 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PEG10 | NM_001172437.2 | c.439C>A | p.Pro147Thr | missense_variant | Exon 2 of 2 | NP_001165908.1 | ||
PEG10 | NM_001184961.1 | c.313C>A | p.Pro105Thr | missense_variant | Exon 2 of 2 | NP_001171890.1 | ||
PEG10 | NM_015068.3 | c.211C>A | p.Pro71Thr | missense_variant | Exon 2 of 2 | NP_055883.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PEG10 | ENST00000612748.1 | c.439C>A | p.Pro147Thr | missense_variant | Exon 2 of 3 | 5 | ENSP00000480676.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000407 AC: 1AN: 245732Hom.: 0 AF XY: 0.00000749 AC XY: 1AN XY: 133466
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1460404Hom.: 0 Cov.: 35 AF XY: 0.00000138 AC XY: 1AN XY: 726398
GnomAD4 genome Cov.: 32
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at