20-45175881-A-C
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_002638.4(PI3):āc.100A>Cā(p.Thr34Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.176 in 1,613,876 control chromosomes in the GnomAD database, including 26,291 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 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_002638.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PI3 | NM_002638.4 | c.100A>C | p.Thr34Pro | missense_variant | 2/3 | ENST00000243924.4 | NP_002629.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PI3 | ENST00000243924.4 | c.100A>C | p.Thr34Pro | missense_variant | 2/3 | 1 | NM_002638.4 | ENSP00000243924 | P1 |
Frequencies
GnomAD3 genomes AF: 0.157 AC: 23921AN: 152048Hom.: 2021 Cov.: 32
GnomAD3 exomes AF: 0.155 AC: 39041AN: 251378Hom.: 3526 AF XY: 0.161 AC XY: 21846AN XY: 135860
GnomAD4 exome AF: 0.177 AC: 259373AN: 1461710Hom.: 24265 Cov.: 33 AF XY: 0.177 AC XY: 128810AN XY: 727160
GnomAD4 genome AF: 0.157 AC: 23960AN: 152166Hom.: 2026 Cov.: 32 AF XY: 0.158 AC XY: 11740AN XY: 74398
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at