chr20-25296515-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_002862.4(PYGB):c.2525G>A(p.Arg842Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000285 in 1,612,732 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_002862.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PYGB | NM_002862.4 | c.2525G>A | p.Arg842Gln | missense_variant | 20/20 | ENST00000216962.9 | |
ABHD12 | NM_015600.5 | c.1158-1485C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PYGB | ENST00000216962.9 | c.2525G>A | p.Arg842Gln | missense_variant | 20/20 | 1 | NM_002862.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152138Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000160 AC: 4AN: 249788Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135036
GnomAD4 exome AF: 0.0000301 AC: 44AN: 1460594Hom.: 0 Cov.: 31 AF XY: 0.0000317 AC XY: 23AN XY: 726528
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152138Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74312
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 12, 2022 | The c.2525G>A (p.R842Q) alteration is located in exon 20 (coding exon 20) of the PYGB gene. This alteration results from a G to A substitution at nucleotide position 2525, causing the arginine (R) at amino acid position 842 to be replaced by a glutamine (Q). 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