chr5-149826745-G-A
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_133263.4(PPARGC1B):c.325G>A(p.Gly109Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000148 in 1,613,906 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_133263.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PPARGC1B | NM_133263.4 | c.325G>A | p.Gly109Ser | missense_variant | 3/12 | ENST00000309241.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PPARGC1B | ENST00000309241.10 | c.325G>A | p.Gly109Ser | missense_variant | 3/12 | 1 | NM_133263.4 | P2 | |
PPARGC1B | ENST00000394320.7 | c.325G>A | p.Gly109Ser | missense_variant | 3/11 | 1 | A2 | ||
PPARGC1B | ENST00000360453.8 | c.325G>A | p.Gly109Ser | missense_variant | 3/11 | 1 | A2 | ||
PPARGC1B | ENST00000403750.5 | c.250G>A | p.Gly84Ser | missense_variant | 3/11 | 2 | A2 |
Frequencies
GnomAD3 genomes AF: 0.000230 AC: 35AN: 152068Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000302 AC: 76AN: 251410Hom.: 1 AF XY: 0.000287 AC XY: 39AN XY: 135892
GnomAD4 exome AF: 0.000140 AC: 204AN: 1461838Hom.: 2 Cov.: 32 AF XY: 0.000142 AC XY: 103AN XY: 727228
GnomAD4 genome AF: 0.000230 AC: 35AN: 152068Hom.: 0 Cov.: 33 AF XY: 0.000175 AC XY: 13AN XY: 74282
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 21, 2021 | The c.325G>A (p.G109S) alteration is located in exon 3 (coding exon 3) of the PPARGC1B gene. This alteration results from a G to A substitution at nucleotide position 325, causing the glycine (G) at amino acid position 109 to be replaced by a serine (S). 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