chr2-71202531-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_020459.1(PAIP2B):c.59G>A(p.Gly20Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000821 in 1,461,536 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_020459.1 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 |
---|---|---|---|---|---|---|---|---|
PAIP2B | NM_020459.1 | c.59G>A | p.Gly20Glu | missense_variant | Exon 2 of 4 | ENST00000244221.9 | NP_065192.1 | |
PAIP2B | XM_011532842.4 | c.122G>A | p.Gly41Glu | missense_variant | Exon 2 of 4 | XP_011531144.1 | ||
PAIP2B | XM_005264310.5 | c.59G>A | p.Gly20Glu | missense_variant | Exon 3 of 5 | XP_005264367.1 | ||
PAIP2B | XM_005264311.5 | c.59G>A | p.Gly20Glu | missense_variant | Exon 2 of 4 | XP_005264368.1 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.0000160 AC: 4AN: 249284Hom.: 0 AF XY: 0.00000739 AC XY: 1AN XY: 135238
GnomAD4 exome AF: 0.00000821 AC: 12AN: 1461536Hom.: 0 Cov.: 30 AF XY: 0.00000550 AC XY: 4AN XY: 727056
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.59G>A (p.G20E) alteration is located in exon 2 (coding exon 1) of the PAIP2B gene. This alteration results from a G to A substitution at nucleotide position 59, causing the glycine (G) at amino acid position 20 to be replaced by a glutamic acid (E). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at