rs3736265
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_013261.5(PPARGC1A):c.1835C>T(p.Thr612Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0656 in 1,613,862 control chromosomes in the GnomAD database, including 4,479 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_013261.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PPARGC1A | NM_013261.5 | c.1835C>T | p.Thr612Met | missense_variant | 9/13 | ENST00000264867.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PPARGC1A | ENST00000264867.7 | c.1835C>T | p.Thr612Met | missense_variant | 9/13 | 1 | NM_013261.5 | P1 | |
PPARGC1A | ENST00000613098.4 | c.1454C>T | p.Thr485Met | missense_variant | 8/12 | 1 | |||
PPARGC1A | ENST00000506055.5 | c.*1050C>T | 3_prime_UTR_variant, NMD_transcript_variant | 9/13 | 1 | ||||
PPARGC1A | ENST00000509702.5 | n.1875C>T | non_coding_transcript_exon_variant | 9/15 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0726 AC: 11040AN: 152076Hom.: 458 Cov.: 31
GnomAD3 exomes AF: 0.0860 AC: 21604AN: 251286Hom.: 1170 AF XY: 0.0873 AC XY: 11852AN XY: 135790
GnomAD4 exome AF: 0.0649 AC: 94876AN: 1461668Hom.: 4021 Cov.: 32 AF XY: 0.0668 AC XY: 48598AN XY: 727152
GnomAD4 genome AF: 0.0725 AC: 11040AN: 152194Hom.: 458 Cov.: 31 AF XY: 0.0779 AC XY: 5792AN XY: 74398
ClinVar
Submissions by phenotype
PPARGC1A-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Feb 22, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at