chr4-23813787-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_013261.5(PPARGC1A):c.1696C>T(p.Arg566Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00174 in 1,612,860 control chromosomes in the GnomAD database, including 34 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 -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PPARGC1A | NM_013261.5 | c.1696C>T | p.Arg566Cys | missense_variant | 8/13 | ENST00000264867.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PPARGC1A | ENST00000264867.7 | c.1696C>T | p.Arg566Cys | missense_variant | 8/13 | 1 | NM_013261.5 | P1 | |
PPARGC1A | ENST00000613098.4 | c.1315C>T | p.Arg439Cys | missense_variant | 7/12 | 1 | |||
PPARGC1A | ENST00000506055.5 | c.*911C>T | 3_prime_UTR_variant, NMD_transcript_variant | 8/13 | 1 | ||||
PPARGC1A | ENST00000509702.5 | n.1736C>T | non_coding_transcript_exon_variant | 8/15 | 5 |
Frequencies
GnomAD3 genomes AF: 0.00755 AC: 1148AN: 152104Hom.: 11 Cov.: 33
GnomAD3 exomes AF: 0.00240 AC: 602AN: 251156Hom.: 9 AF XY: 0.00213 AC XY: 289AN XY: 135712
GnomAD4 exome AF: 0.00114 AC: 1660AN: 1460638Hom.: 23 Cov.: 30 AF XY: 0.00109 AC XY: 791AN XY: 726720
GnomAD4 genome AF: 0.00755 AC: 1150AN: 152222Hom.: 11 Cov.: 33 AF XY: 0.00770 AC XY: 573AN XY: 74418
ClinVar
Submissions by phenotype
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