chr4-23814255-G-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_013261.5(PPARGC1A):c.1228C>A(p.Leu410Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00133 in 1,614,034 control chromosomes in the GnomAD database, including 27 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_013261.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PPARGC1A | NM_013261.5 | c.1228C>A | p.Leu410Ile | missense_variant | 8/13 | ENST00000264867.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PPARGC1A | ENST00000264867.7 | c.1228C>A | p.Leu410Ile | missense_variant | 8/13 | 1 | NM_013261.5 | P1 | |
PPARGC1A | ENST00000613098.4 | c.847C>A | p.Leu283Ile | missense_variant | 7/12 | 1 | |||
PPARGC1A | ENST00000506055.5 | c.*443C>A | 3_prime_UTR_variant, NMD_transcript_variant | 8/13 | 1 | ||||
PPARGC1A | ENST00000509702.5 | n.1268C>A | non_coding_transcript_exon_variant | 8/15 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00571 AC: 869AN: 152086Hom.: 8 Cov.: 32
GnomAD3 exomes AF: 0.00177 AC: 445AN: 250828Hom.: 1 AF XY: 0.00147 AC XY: 199AN XY: 135542
GnomAD4 exome AF: 0.000867 AC: 1268AN: 1461830Hom.: 18 Cov.: 70 AF XY: 0.000814 AC XY: 592AN XY: 727220
GnomAD4 genome ? AF: 0.00574 AC: 874AN: 152204Hom.: 9 Cov.: 32 AF XY: 0.00554 AC XY: 412AN XY: 74402
ClinVar
Submissions by phenotype
PPARGC1A-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | May 24, 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). - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jun 05, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at