4-23801889-G-A
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_013261.5(PPARGC1A):c.2142-8C>T variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0003 in 1,613,676 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_013261.5 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PPARGC1A | NM_013261.5 | c.2142-8C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000264867.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PPARGC1A | ENST00000264867.7 | c.2142-8C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_013261.5 | P1 | |||
PPARGC1A | ENST00000613098.4 | c.1761-8C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | |||||
PPARGC1A | ENST00000506055.5 | c.*1357-8C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant, NMD_transcript_variant | 1 | |||||
PPARGC1A | ENST00000509702.5 | n.2182-8C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.00114 AC: 174AN: 152130Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000678 AC: 169AN: 249404Hom.: 0 AF XY: 0.000712 AC XY: 96AN XY: 134908
GnomAD4 exome AF: 0.000212 AC: 310AN: 1461428Hom.: 0 Cov.: 31 AF XY: 0.000256 AC XY: 186AN XY: 727028
GnomAD4 genome AF: 0.00114 AC: 174AN: 152248Hom.: 0 Cov.: 32 AF XY: 0.00167 AC XY: 124AN XY: 74406
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | May 21, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at