chr4-23814170-A-G
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_013261.5(PPARGC1A):āc.1313T>Cā(p.Leu438Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00172 in 1,614,092 control chromosomes in the GnomAD database, including 36 homozygotes. 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 Benign (ā ā ).
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.1313T>C | p.Leu438Ser | missense_variant | 8/13 | ENST00000264867.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PPARGC1A | ENST00000264867.7 | c.1313T>C | p.Leu438Ser | missense_variant | 8/13 | 1 | NM_013261.5 | P1 | |
PPARGC1A | ENST00000613098.4 | c.932T>C | p.Leu311Ser | missense_variant | 7/12 | 1 | |||
PPARGC1A | ENST00000506055.5 | c.*528T>C | 3_prime_UTR_variant, NMD_transcript_variant | 8/13 | 1 | ||||
PPARGC1A | ENST00000509702.5 | n.1353T>C | non_coding_transcript_exon_variant | 8/15 | 5 |
Frequencies
GnomAD3 genomes AF: 0.00771 AC: 1173AN: 152128Hom.: 12 Cov.: 32
GnomAD3 exomes AF: 0.00236 AC: 592AN: 250894Hom.: 10 AF XY: 0.00209 AC XY: 284AN XY: 135562
GnomAD4 exome AF: 0.00109 AC: 1594AN: 1461846Hom.: 24 Cov.: 69 AF XY: 0.00105 AC XY: 761AN XY: 727218
GnomAD4 genome AF: 0.00772 AC: 1176AN: 152246Hom.: 12 Cov.: 32 AF XY: 0.00786 AC XY: 585AN XY: 74440
ClinVar
Submissions by phenotype
PPARGC1A-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jul 29, 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 | Jul 05, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at